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From: Chipster <chi...@cs...> - 2025-09-19 07:17:53
|
Hi Chipster admins, Chipster has used Bitnami image to run its PostgreSQL databases. Unfortunately, Bitnami has decided to stop maintaining this image after September 29th: https://hub.docker.com/r/bitnami/postgresql . Your current Chipster installation should have pulled the old image and should continue working even after this date, but new installations of old Chipster versions won’t anymore find the database image. This is fixed in Chipster version v4.18.0, but the update requires a few extra steps. When you decide to update, please follow the update instructions in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#replace-bitnami-image . Best regards, Petri / Chipster Team -- Petri Klemelä Chipster Team, CSC – IT Center for Science chi...@cs... The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy> Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja> |
|
From: Chipster <chi...@cs...> - 2025-07-23 08:41:06
|
Thanks for reporting back, I’m happy to hear that there was again a sensible explanation for this!
Best regards,
Petri / Chipster Team
--
Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...
From: Oliver Heil <o....@dk...>
Date: Wednesday, 23. July 2025 at 11.32
To: chi...@li... <chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
Dear Petry,
chipsterVM1 is up and running again!
Thanx a lot (as usual) :-D
we learned: renaming to ...yaml.BACKUP is not enough to deactivate :-D
I wish you all good times!
Oli
Am 23.07.2025 um 09:54 schrieb Chipster:
Hi Oli,
yay, finally this makes sense. There are two extra files:
helm/chipster/templates/ingress.yaml.backup
helm/chipster/values.yaml.backup
Those are probably copies of some older version of the ingress.yaml and values.yaml. Helm apparently finds them and tries to deploy them, causing problems with their old API definitions. I may have even instructed you to create these files at some point without realising that Helm will find them.
When we run the command “git pull” to get the latest versions, it doesn’t warn about those files, because it assumes those are your modifications that you want to keep.
Please delete or move those two files outside of helm directory, where Helm can’t find them. After that it’s probably best to uninstall K3s once more to remove all old crud and install K3s and Chipster again.
--
Oliver Heil (er/ihm,he/him)
Microarray Core Facility
Bioinformatics
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
o....@dk...<mailto:o....@dk...>
Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/>
www.dkfz.de<http://www.dkfz.de>
[Research for a Life without Cancer]
Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy>
Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja>
|
|
From: Oliver H. <o....@dk...> - 2025-07-23 08:31:40
|
Dear Petry, chipsterVM1 is up and running again! Thanx a lot (as usual) :-D we learned: renaming to ...yaml.BACKUP is not enough to deactivate :-D I wish you all good times! Oli Am 23.07.2025 um 09:54 schrieb Chipster: > > Hi Oli, > > yay, finally this makes sense. There are two extra files: > > helm/chipster/templates/ingress.yaml.backup > > helm/chipster/values.yaml.backup > > Those are probably copies of some older version of the ingress.yaml > and values.yaml. Helm apparently finds them and tries to deploy them, > causing problems with their old API definitions. I may have even > instructed you to create these files at some point without realising > that Helm will find them. > > When we run the command “git pull” to get the latest versions, it > doesn’t warn about those files, because it assumes those are your > modifications that you want to keep. > > Please delete or move those two files outside of helm directory, where > Helm can’t find them. After that it’s probably best to uninstall K3s > once more to remove all old crud and install K3s and Chipster again. > -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
|
From: Chipster <chi...@cs...> - 2025-07-23 07:55:08
|
Hi Oli,
yay, finally this makes sense. There are two extra files:
helm/chipster/templates/ingress.yaml.backup
helm/chipster/values.yaml.backup
Those are probably copies of some older version of the ingress.yaml and values.yaml. Helm apparently finds them and tries to deploy them, causing problems with their old API definitions. I may have even instructed you to create these files at some point without realising that Helm will find them.
When we run the command “git pull” to get the latest versions, it doesn’t warn about those files, because it assumes those are your modifications that you want to keep.
Please delete or move those two files outside of helm directory, where Helm can’t find them. After that it’s probably best to uninstall K3s once more to remove all old crud and install K3s and Chipster again.
Best regards,
Petri / Chipster Team
--
Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...
From: Oliver Heil <o....@dk...>
Date: Wednesday, 23. July 2025 at 10.23
To: chi...@li... <chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
Ah perhaps here is something wrong:
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git status
HEAD detached at v4.15.0
Untracked files:
(use "git add <file>..." to include in what will be committed)
helm/chipster/Chart.lock
helm/chipster/charts/
helm/chipster/templates/ingress.yaml.backup
helm/chipster/values.yaml.backup
nothing added to commit but untracked files present (use "git add" to track)
Am 23.07.2025 um 07:34 schrieb Chipster:
Hi Oli,
I got your email through the email list eventually, so apparently the list just had some temporary glitch.
I guess missing IngressRoutes and Middlewares are expected, because that’s where the deployment fails.
** Let’s check that you don’t have any local changes in those files:
$ git status
On branch k3s
Your branch is up to date with 'origin/k3s'.
Untracked files:
(use "git add <file>..." to include in what will be committed)
k3s/helm/chipster/Chart.lock
k3s/helm/chipster/charts/
nothing added to commit but untracked files present (use "git add" to track)
** If there are changes, you can check those with
$ git diff <file_path>
Best regards,
Petri / Chipster Team
--
Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...<mailto:chi...@cs...>
From: Oliver Heil <o....@dk...><mailto:o....@dk...>
Date: Tuesday, 22. July 2025 at 15.25
To: chi...@li...<mailto:chi...@li...> <chi...@li...><mailto:chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
Problems start with the ingress thing:
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git log
commit 46016f41f46905bb7fc2390b5d188464fc6b27da (HEAD, tag: v4.15.0, origin/k3s-ubuntu24, origin/k3s, k3s)
Author: Petri Klemela <pet...@cs...><mailto:pet...@cs...>
Date: Wed May 14 09:41:59 2025 +0300
Fix typo
commit d590b6d6ba349f2a7384ebd31491be1614237974
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ k3s -v
k3s version v1.32.4+k3s1 (6b330558)
go version go1.23.6
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get namespace
NAME STATUS AGE
default Active 36m
kube-node-lease Active 36m
kube-public Active 36m
kube-system Active 36m
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get ingressroute
No resources found in default namespace.
===================^^^^^^^^^^^^^^^^^^^^
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get middleware
No resources found in default namespace.
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get node
NAME STATUS ROLES AGE VERSION
chipstervm1 Ready control-plane,master 37m v1.32.4+k3s1
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ hostname
chipstervm1
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ journalctl -u k3s.service --no-pager | grep "database"
Jun 18 10:20:36 chipstervm1 k3s[956]: time="2025-06-18T10:20:36+02:00" level=error msg="Compact failed: failed to compact to revision 41449638: database is locked"
Jun 20 01:45:36 chipstervm1 k3s[956]: time="2025-06-20T01:45:36+02:00" level=error msg="Compact failed: failed to compact to revision 41492579: database is locked"
Jun 24 11:25:36 chipstervm1 k3s[956]: time="2025-06-24T11:25:36+02:00" level=error msg="Compact failed: failed to compact to revision 41607701: database is locked"
Jun 28 23:20:36 chipstervm1 k3s[956]: time="2025-06-28T23:20:36+02:00" level=error msg="Compact failed: failed to compact to revision 41725264: database is locked"
Jun 30 18:35:36 chipstervm1 k3s[956]: time="2025-06-30T18:35:36+02:00" level=error msg="Compact failed: failed to compact to revision 41772386: database is locked"
Jul 07 15:02:12 chipstervm1 k3s[747637]: time="2025-07-07T15:02:12+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:02:12 chipstervm1 k3s[747637]: time="2025-07-07T15:02:12+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1295288538]: ---"Object deleted from database" 524ms (15:04:56.387)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[337602364]: ---"Object deleted from database" 542ms (15:04:56.413)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[147515258]: ---"Object deleted from database" 510ms (15:04:56.423)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[605196751]: ---"Object deleted from database" 521ms (15:04:56.428)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1750733902]: ---"Object deleted from database" 536ms (15:04:56.432)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[270507439]: ---"Object deleted from database" 570ms (15:04:56.440)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[513417525]: ---"Object deleted from database" 558ms (15:04:56.448)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[546947458]: ---"Object deleted from database" 590ms (15:04:56.453)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1353657320]: ---"Object deleted from database" 593ms (15:04:56.458)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1180849967]: ---"Object deleted from database" 600ms (15:04:56.465)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[512674873]: ---"Object deleted from database" 567ms (15:04:56.470)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1416147340]: ---"Object deleted from database" 574ms (15:04:56.475)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1199243352]: ---"Object deleted from database" 605ms (15:04:56.479)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[669529128]: ---"Object deleted from database" 600ms (15:04:56.483)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1342959763]: ---"Object deleted from database" 609ms (15:04:56.488)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1214239173]: ---"Object deleted from database" 580ms (15:04:56.493)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[783574743]: ---"Object deleted from database" 584ms (15:04:56.498)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1600294098]: ---"Object deleted from database" 595ms (15:04:56.502)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[985792831]: ---"Object deleted from database" 620ms (15:04:56.506)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1107874578]: ---"Object deleted from database" 634ms (15:04:56.510)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[406458206]: ---"Object deleted from database" 616ms (15:04:56.515)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[654409944]: ---"Object deleted from database" 652ms (15:04:56.519)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[2001160119]: ---"Object deleted from database" 631ms (15:04:56.523)
Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 16:14:21 chipstervm1 k3s[1046]: time="2025-07-07T16:14:21+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 16:14:21 chipstervm1 k3s[1046]: time="2025-07-07T16:14:21+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 16:17:55 chipstervm1 k3s[4218]: time="2025-07-07T16:17:55+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 16:17:55 chipstervm1 k3s[4218]: time="2025-07-07T16:17:55+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 22 10:58:21 chipstervm1 k3s[1032]: time="2025-07-22T10:58:21+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 22 10:58:21 chipstervm1 k3s[1032]: time="2025-07-22T10:58:21+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 22 13:18:00 chipstervm1 k3s[11626]: time="2025-07-22T13:18:00+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 22 13:18:00 chipstervm1 k3s[11626]: time="2025-07-22T13:18:00+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ sudo ls -l /var/lib/rancher/k3s/server/db/
[sudo] password for ubuntu:
total 12056
drwx------ 2 root root 4096 Jul 22 13:18 etcd
-rw-r--r-- 1 root root 7655424 Jul 22 13:58 state.db
-rw-r--r-- 1 root root 32768 Jul 22 13:59 state.db-shm
-rw-r--r-- 1 root root 4647392 Jul 22 13:59 state.db-wal
Am 22.07.2025 um 13:52 schrieb Chipster:
Hi Oli,
well, that’s certainly interesting. Let’s find out what’s the difference.
--
Oliver Heil (er/ihm,he/him)
Microarray Core Facility
Bioinformatics
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
o....@dk...<mailto:o....@dk...>
Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/>
www.dkfz.de<http://www.dkfz.de>
[Research for a Life without Cancer]
Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy>
Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja>
--
Oliver Heil (er/ihm,he/him)
Microarray Core Facility
Bioinformatics
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
o....@dk...<mailto:o....@dk...>
Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/>
www.dkfz.de<http://www.dkfz.de>
[Research for a Life without Cancer]
Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
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From: Oliver H. <o....@dk...> - 2025-07-23 07:23:26
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On the working VM it's nearly the same, so perhaps not the problem: > ubuntu@chipstervm2:~/git/chipster-openshift/k3s$ git status > HEAD detached at v4.15.0 > Untracked files: > (use "git add <file>..." to include in what will be committed) > helm/chipster/Chart.lock > helm/chipster/charts/ > > nothing added to commit but untracked files present (use "git add" to > track) Am 23.07.2025 um 09:06 schrieb Oliver Heil: > > Ah perhaps here is something wrong: > > >> ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git status >> HEAD detached at v4.15.0 >> Untracked files: >> (use "git add <file>..." to include in what will be committed) >> helm/chipster/Chart.lock >> helm/chipster/charts/ >> helm/chipster/templates/ingress.yaml.backup >> helm/chipster/values.yaml.backup >> >> nothing added to commit but untracked files present (use "git add" to >> track) > > > -- > > Oliver Heil (er/ihm,he/him) > Microarray Core Facility > Bioinformatics > > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > > o....@dk... <mailto:o....@dk...> > Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> > www.dkfz.de <http://www.dkfz.de> > > Research for a Life without Cancer > > Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich > VAT-ID No.: DE143293537 > > > > _______________________________________________ > Chipster-tech mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-tech -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
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From: Oliver H. <o....@dk...> - 2025-07-23 07:06:33
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Ah perhaps here is something wrong: > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git status > HEAD detached at v4.15.0 > Untracked files: > (use "git add <file>..." to include in what will be committed) > helm/chipster/Chart.lock > helm/chipster/charts/ > helm/chipster/templates/ingress.yaml.backup > helm/chipster/values.yaml.backup > > nothing added to commit but untracked files present (use "git add" to > track) Am 23.07.2025 um 07:34 schrieb Chipster: > > Hi Oli, > > I got your email through the email list eventually, so apparently the > list just had some temporary glitch. > > I guess missing IngressRoutes and Middlewares are expected, because > that’s where the deployment fails. > > ** Let’s check that you don’t have any local changes in those files: > > $ git status > > On branch k3s > > Your branch is up to date with 'origin/k3s'. > > Untracked files: > > (use "git add <file>..." to include in what will be committed) > > k3s/helm/chipster/Chart.lock > > k3s/helm/chipster/charts/ > > nothing added to commit but untracked files present (use "git add" to > track) > > ** If there are changes, you can check those with > > $ git diff <file_path> > > Best regards, > > Petri / Chipster Team > > -- > > Petri Klemelä > > Chipster Team, CSC – IT Center for Science > > chi...@cs... > > *From: *Oliver Heil <o....@dk...> > *Date: *Tuesday, 22. July 2025 at 15.25 > *To: *chi...@li... > <chi...@li...> > *Subject: *Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 > updates in Chipster > -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
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From: Oliver H. <o....@dk...> - 2025-07-23 06:53:11
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Ah perhaps here is something wrong: > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git status > HEAD detached at v4.15.0 > Untracked files: > (use "git add <file>..." to include in what will be committed) > helm/chipster/Chart.lock > helm/chipster/charts/ > helm/chipster/templates/ingress.yaml.backup > helm/chipster/values.yaml.backup > > nothing added to commit but untracked files present (use "git add" to > track) Am 23.07.2025 um 07:34 schrieb Chipster: > > Hi Oli, > > I got your email through the email list eventually, so apparently the > list just had some temporary glitch. > > I guess missing IngressRoutes and Middlewares are expected, because > that’s where the deployment fails. > > ** Let’s check that you don’t have any local changes in those files: > > $ git status > > On branch k3s > > Your branch is up to date with 'origin/k3s'. > > Untracked files: > > (use "git add <file>..." to include in what will be committed) > > k3s/helm/chipster/Chart.lock > > k3s/helm/chipster/charts/ > > nothing added to commit but untracked files present (use "git add" to > track) > > ** If there are changes, you can check those with > > $ git diff <file_path> > > Best regards, > > Petri / Chipster Team > > -- > > Petri Klemelä > > Chipster Team, CSC – IT Center for Science > > chi...@cs... > > *From: *Oliver Heil <o....@dk...> > *Date: *Tuesday, 22. July 2025 at 15.25 > *To: *chi...@li... > <chi...@li...> > *Subject: *Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 > updates in Chipster > > Problems start with the ingress thing: > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git log > commit 46016f41f46905bb7fc2390b5d188464fc6b27da (HEAD, tag: > v4.15.0, origin/k3s-ubuntu24, origin/k3s, k3s) > Author: Petri Klemela <pet...@cs...> > <mailto:pet...@cs...> > Date: Wed May 14 09:41:59 2025 +0300 > > Fix typo > > commit d590b6d6ba349f2a7384ebd31491be1614237974 > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ k3s -v > k3s version v1.32.4+k3s1 (6b330558) > go version go1.23.6 > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get namespace > NAME STATUS AGE > default Active 36m > kube-node-lease Active 36m > kube-public Active 36m > kube-system Active 36m > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get > ingressroute > No resources found in default namespace. > > ===================^^^^^^^^^^^^^^^^^^^^ > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get > middleware > No resources found in default namespace. > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get node > NAME STATUS ROLES AGE VERSION > chipstervm1 Ready control-plane,master 37m v1.32.4+k3s1 > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ hostname > chipstervm1 > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ journalctl -u > k3s.service --no-pager | grep "database" > Jun 18 10:20:36 chipstervm1 k3s[956]: > time="2025-06-18T10:20:36+02:00" level=error msg="Compact failed: > failed to compact to revision 41449638: database is locked" > Jun 20 01:45:36 chipstervm1 k3s[956]: > time="2025-06-20T01:45:36+02:00" level=error msg="Compact failed: > failed to compact to revision 41492579: database is locked" > Jun 24 11:25:36 chipstervm1 k3s[956]: > time="2025-06-24T11:25:36+02:00" level=error msg="Compact failed: > failed to compact to revision 41607701: database is locked" > Jun 28 23:20:36 chipstervm1 k3s[956]: > time="2025-06-28T23:20:36+02:00" level=error msg="Compact failed: > failed to compact to revision 41725264: database is locked" > Jun 30 18:35:36 chipstervm1 k3s[956]: > time="2025-06-30T18:35:36+02:00" level=error msg="Compact failed: > failed to compact to revision 41772386: database is locked" > Jul 07 15:02:12 chipstervm1 k3s[747637]: > time="2025-07-07T15:02:12+02:00" level=info msg="Configuring > sqlite3 database connection pooling: maxIdleConns=2, > maxOpenConns=0, connMaxLifetime=0s" > Jul 07 15:02:12 chipstervm1 k3s[747637]: > time="2025-07-07T15:02:12+02:00" level=info msg="Configuring > database table schema and indexes, this may take a moment..." > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1295288538]: > ---"Object deleted from database" 524ms (15:04:56.387) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[337602364]: > ---"Object deleted from database" 542ms (15:04:56.413) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[147515258]: > ---"Object deleted from database" 510ms (15:04:56.423) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[605196751]: > ---"Object deleted from database" 521ms (15:04:56.428) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1750733902]: > ---"Object deleted from database" 536ms (15:04:56.432) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[270507439]: > ---"Object deleted from database" 570ms (15:04:56.440) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[513417525]: > ---"Object deleted from database" 558ms (15:04:56.448) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[546947458]: > ---"Object deleted from database" 590ms (15:04:56.453) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1353657320]: > ---"Object deleted from database" 593ms (15:04:56.458) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1180849967]: > ---"Object deleted from database" 600ms (15:04:56.465) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[512674873]: > ---"Object deleted from database" 567ms (15:04:56.470) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1416147340]: > ---"Object deleted from database" 574ms (15:04:56.475) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1199243352]: > ---"Object deleted from database" 605ms (15:04:56.479) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[669529128]: > ---"Object deleted from database" 600ms (15:04:56.483) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1342959763]: > ---"Object deleted from database" 609ms (15:04:56.488) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1214239173]: > ---"Object deleted from database" 580ms (15:04:56.493) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[783574743]: > ---"Object deleted from database" 584ms (15:04:56.498) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1600294098]: > ---"Object deleted from database" 595ms (15:04:56.502) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[985792831]: > ---"Object deleted from database" 620ms (15:04:56.506) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1107874578]: > ---"Object deleted from database" 634ms (15:04:56.510) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[406458206]: > ---"Object deleted from database" 616ms (15:04:56.515) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[654409944]: > ---"Object deleted from database" 652ms (15:04:56.519) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[2001160119]: > ---"Object deleted from database" 631ms (15:04:56.523) > Jul 07 15:09:50 chipstervm1 k3s[935]: > time="2025-07-07T15:09:50+02:00" level=info msg="Configuring > sqlite3 database connection pooling: maxIdleConns=2, > maxOpenConns=0, connMaxLifetime=0s" > Jul 07 15:09:50 chipstervm1 k3s[935]: > time="2025-07-07T15:09:50+02:00" level=info msg="Configuring > database table schema and indexes, this may take a moment..." > Jul 07 15:48:41 chipstervm1 k3s[918]: > time="2025-07-07T15:48:41+02:00" level=info msg="Configuring > sqlite3 database connection pooling: maxIdleConns=2, > maxOpenConns=0, connMaxLifetime=0s" > Jul 07 15:48:41 chipstervm1 k3s[918]: > time="2025-07-07T15:48:41+02:00" level=info msg="Configuring > database table schema and indexes, this may take a moment..." > Jul 07 16:14:21 chipstervm1 k3s[1046]: > time="2025-07-07T16:14:21+02:00" level=info msg="Configuring > sqlite3 database connection pooling: maxIdleConns=2, > maxOpenConns=0, connMaxLifetime=0s" > Jul 07 16:14:21 chipstervm1 k3s[1046]: > time="2025-07-07T16:14:21+02:00" level=info msg="Configuring > database table schema and indexes, this may take a moment..." > Jul 07 16:17:55 chipstervm1 k3s[4218]: > time="2025-07-07T16:17:55+02:00" level=info msg="Configuring > sqlite3 database connection pooling: maxIdleConns=2, > maxOpenConns=0, connMaxLifetime=0s" > Jul 07 16:17:55 chipstervm1 k3s[4218]: > time="2025-07-07T16:17:55+02:00" level=info msg="Configuring > database table schema and indexes, this may take a moment..." > Jul 22 10:58:21 chipstervm1 k3s[1032]: > time="2025-07-22T10:58:21+02:00" level=info msg="Configuring > sqlite3 database connection pooling: maxIdleConns=2, > maxOpenConns=0, connMaxLifetime=0s" > Jul 22 10:58:21 chipstervm1 k3s[1032]: > time="2025-07-22T10:58:21+02:00" level=info msg="Configuring > database table schema and indexes, this may take a moment..." > Jul 22 13:18:00 chipstervm1 k3s[11626]: > time="2025-07-22T13:18:00+02:00" level=info msg="Configuring > sqlite3 database connection pooling: maxIdleConns=2, > maxOpenConns=0, connMaxLifetime=0s" > Jul 22 13:18:00 chipstervm1 k3s[11626]: > time="2025-07-22T13:18:00+02:00" level=info msg="Configuring > database table schema and indexes, this may take a moment..." > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ sudo ls -l > /var/lib/rancher/k3s/server/db/ > [sudo] password for ubuntu: > total 12056 > drwx------ 2 root root 4096 Jul 22 13:18 etcd > -rw-r--r-- 1 root root 7655424 Jul 22 13:58 state.db > -rw-r--r-- 1 root root 32768 Jul 22 13:59 state.db-shm > -rw-r--r-- 1 root root 4647392 Jul 22 13:59 state.db-wal > > > > Am 22.07.2025 um 13:52 schrieb Chipster: > > Hi Oli, > > well, that’s certainly interesting. Let’s find out what’s the > difference. > > -- > > Oliver Heil (er/ihm,he/him) > Microarray Core Facility > Bioinformatics > > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > > o....@dk... <mailto:o....@dk...> > Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> > www.dkfz.de <http://www.dkfz.de> > > Research for a Life without Cancer > > Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich > VAT-ID No.: DE143293537 > > > > /The information in this email may be confidential and is intended > solely for the use of the individual or entity to whom it is intended. > If you are not the intended recipient of this message, please delete > the message and notify the sender immediately. For information on how > we process personal data and our contact information, please see CSC's > website: Privacy <https://csc.fi/en/privacy> > > Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on > tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on > osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa > viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja > henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n > verkkosivuilta: Tietosuoja <https://csc.fi/tietosuoja> / -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
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From: Chipster <chi...@cs...> - 2025-07-23 05:35:05
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Hi Oli,
I got your email through the email list eventually, so apparently the list just had some temporary glitch.
I guess missing IngressRoutes and Middlewares are expected, because that’s where the deployment fails.
** Let’s check that you don’t have any local changes in those files:
$ git status
On branch k3s
Your branch is up to date with 'origin/k3s'.
Untracked files:
(use "git add <file>..." to include in what will be committed)
k3s/helm/chipster/Chart.lock
k3s/helm/chipster/charts/
nothing added to commit but untracked files present (use "git add" to track)
** If there are changes, you can check those with
$ git diff <file_path>
Best regards,
Petri / Chipster Team
--
Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...
From: Oliver Heil <o....@dk...>
Date: Tuesday, 22. July 2025 at 15.25
To: chi...@li... <chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
Problems start with the ingress thing:
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git log
commit 46016f41f46905bb7fc2390b5d188464fc6b27da (HEAD, tag: v4.15.0, origin/k3s-ubuntu24, origin/k3s, k3s)
Author: Petri Klemela <pet...@cs...><mailto:pet...@cs...>
Date: Wed May 14 09:41:59 2025 +0300
Fix typo
commit d590b6d6ba349f2a7384ebd31491be1614237974
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ k3s -v
k3s version v1.32.4+k3s1 (6b330558)
go version go1.23.6
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get namespace
NAME STATUS AGE
default Active 36m
kube-node-lease Active 36m
kube-public Active 36m
kube-system Active 36m
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get ingressroute
No resources found in default namespace.
===================^^^^^^^^^^^^^^^^^^^^
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get middleware
No resources found in default namespace.
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get node
NAME STATUS ROLES AGE VERSION
chipstervm1 Ready control-plane,master 37m v1.32.4+k3s1
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ hostname
chipstervm1
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ journalctl -u k3s.service --no-pager | grep "database"
Jun 18 10:20:36 chipstervm1 k3s[956]: time="2025-06-18T10:20:36+02:00" level=error msg="Compact failed: failed to compact to revision 41449638: database is locked"
Jun 20 01:45:36 chipstervm1 k3s[956]: time="2025-06-20T01:45:36+02:00" level=error msg="Compact failed: failed to compact to revision 41492579: database is locked"
Jun 24 11:25:36 chipstervm1 k3s[956]: time="2025-06-24T11:25:36+02:00" level=error msg="Compact failed: failed to compact to revision 41607701: database is locked"
Jun 28 23:20:36 chipstervm1 k3s[956]: time="2025-06-28T23:20:36+02:00" level=error msg="Compact failed: failed to compact to revision 41725264: database is locked"
Jun 30 18:35:36 chipstervm1 k3s[956]: time="2025-06-30T18:35:36+02:00" level=error msg="Compact failed: failed to compact to revision 41772386: database is locked"
Jul 07 15:02:12 chipstervm1 k3s[747637]: time="2025-07-07T15:02:12+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:02:12 chipstervm1 k3s[747637]: time="2025-07-07T15:02:12+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1295288538]: ---"Object deleted from database" 524ms (15:04:56.387)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[337602364]: ---"Object deleted from database" 542ms (15:04:56.413)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[147515258]: ---"Object deleted from database" 510ms (15:04:56.423)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[605196751]: ---"Object deleted from database" 521ms (15:04:56.428)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1750733902]: ---"Object deleted from database" 536ms (15:04:56.432)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[270507439]: ---"Object deleted from database" 570ms (15:04:56.440)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[513417525]: ---"Object deleted from database" 558ms (15:04:56.448)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[546947458]: ---"Object deleted from database" 590ms (15:04:56.453)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1353657320]: ---"Object deleted from database" 593ms (15:04:56.458)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1180849967]: ---"Object deleted from database" 600ms (15:04:56.465)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[512674873]: ---"Object deleted from database" 567ms (15:04:56.470)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1416147340]: ---"Object deleted from database" 574ms (15:04:56.475)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1199243352]: ---"Object deleted from database" 605ms (15:04:56.479)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[669529128]: ---"Object deleted from database" 600ms (15:04:56.483)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1342959763]: ---"Object deleted from database" 609ms (15:04:56.488)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1214239173]: ---"Object deleted from database" 580ms (15:04:56.493)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[783574743]: ---"Object deleted from database" 584ms (15:04:56.498)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1600294098]: ---"Object deleted from database" 595ms (15:04:56.502)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[985792831]: ---"Object deleted from database" 620ms (15:04:56.506)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1107874578]: ---"Object deleted from database" 634ms (15:04:56.510)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[406458206]: ---"Object deleted from database" 616ms (15:04:56.515)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[654409944]: ---"Object deleted from database" 652ms (15:04:56.519)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[2001160119]: ---"Object deleted from database" 631ms (15:04:56.523)
Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 16:14:21 chipstervm1 k3s[1046]: time="2025-07-07T16:14:21+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 16:14:21 chipstervm1 k3s[1046]: time="2025-07-07T16:14:21+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 16:17:55 chipstervm1 k3s[4218]: time="2025-07-07T16:17:55+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 16:17:55 chipstervm1 k3s[4218]: time="2025-07-07T16:17:55+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 22 10:58:21 chipstervm1 k3s[1032]: time="2025-07-22T10:58:21+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 22 10:58:21 chipstervm1 k3s[1032]: time="2025-07-22T10:58:21+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 22 13:18:00 chipstervm1 k3s[11626]: time="2025-07-22T13:18:00+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 22 13:18:00 chipstervm1 k3s[11626]: time="2025-07-22T13:18:00+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ sudo ls -l /var/lib/rancher/k3s/server/db/
[sudo] password for ubuntu:
total 12056
drwx------ 2 root root 4096 Jul 22 13:18 etcd
-rw-r--r-- 1 root root 7655424 Jul 22 13:58 state.db
-rw-r--r-- 1 root root 32768 Jul 22 13:59 state.db-shm
-rw-r--r-- 1 root root 4647392 Jul 22 13:59 state.db-wal
Am 22.07.2025 um 13:52 schrieb Chipster:
Hi Oli,
well, that’s certainly interesting. Let’s find out what’s the difference.
--
Oliver Heil (er/ihm,he/him)
Microarray Core Facility
Bioinformatics
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
o....@dk...<mailto:o....@dk...>
Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/>
www.dkfz.de<http://www.dkfz.de>
[Research for a Life without Cancer]
Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy>
Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja>
|
|
From: Oliver H. <o....@dk...> - 2025-07-22 12:24:43
|
Problems start with the ingress thing: > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git log > commit 46016f41f46905bb7fc2390b5d188464fc6b27da (HEAD, tag: v4.15.0, > origin/k3s-ubuntu24, origin/k3s, k3s) > Author: Petri Klemela <pet...@cs...> > Date: Wed May 14 09:41:59 2025 +0300 > > Fix typo > > commit d590b6d6ba349f2a7384ebd31491be1614237974 > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ k3s -v > k3s version v1.32.4+k3s1 (6b330558) > go version go1.23.6 > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get namespace > NAME STATUS AGE > default Active 36m > kube-node-lease Active 36m > kube-public Active 36m > kube-system Active 36m > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get ingressroute > No resources found in default namespace. ===================^^^^^^^^^^^^^^^^^^^^ > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get middleware > No resources found in default namespace. > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get node > NAME STATUS ROLES AGE VERSION > chipstervm1 Ready control-plane,master 37m v1.32.4+k3s1 > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ hostname > chipstervm1 > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ journalctl -u > k3s.service --no-pager | grep "database" > Jun 18 10:20:36 chipstervm1 k3s[956]: time="2025-06-18T10:20:36+02:00" > level=error msg="Compact failed: failed to compact to revision > 41449638: database is locked" > Jun 20 01:45:36 chipstervm1 k3s[956]: time="2025-06-20T01:45:36+02:00" > level=error msg="Compact failed: failed to compact to revision > 41492579: database is locked" > Jun 24 11:25:36 chipstervm1 k3s[956]: time="2025-06-24T11:25:36+02:00" > level=error msg="Compact failed: failed to compact to revision > 41607701: database is locked" > Jun 28 23:20:36 chipstervm1 k3s[956]: time="2025-06-28T23:20:36+02:00" > level=error msg="Compact failed: failed to compact to revision > 41725264: database is locked" > Jun 30 18:35:36 chipstervm1 k3s[956]: time="2025-06-30T18:35:36+02:00" > level=error msg="Compact failed: failed to compact to revision > 41772386: database is locked" > Jul 07 15:02:12 chipstervm1 k3s[747637]: > time="2025-07-07T15:02:12+02:00" level=info msg="Configuring sqlite3 > database connection pooling: maxIdleConns=2, maxOpenConns=0, > connMaxLifetime=0s" > Jul 07 15:02:12 chipstervm1 k3s[747637]: > time="2025-07-07T15:02:12+02:00" level=info msg="Configuring database > table schema and indexes, this may take a moment..." > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1295288538]: ---"Object > deleted from database" 524ms (15:04:56.387) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[337602364]: ---"Object > deleted from database" 542ms (15:04:56.413) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[147515258]: ---"Object > deleted from database" 510ms (15:04:56.423) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[605196751]: ---"Object > deleted from database" 521ms (15:04:56.428) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1750733902]: ---"Object > deleted from database" 536ms (15:04:56.432) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[270507439]: ---"Object > deleted from database" 570ms (15:04:56.440) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[513417525]: ---"Object > deleted from database" 558ms (15:04:56.448) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[546947458]: ---"Object > deleted from database" 590ms (15:04:56.453) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1353657320]: ---"Object > deleted from database" 593ms (15:04:56.458) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1180849967]: ---"Object > deleted from database" 600ms (15:04:56.465) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[512674873]: ---"Object > deleted from database" 567ms (15:04:56.470) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1416147340]: ---"Object > deleted from database" 574ms (15:04:56.475) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1199243352]: ---"Object > deleted from database" 605ms (15:04:56.479) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[669529128]: ---"Object > deleted from database" 600ms (15:04:56.483) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1342959763]: ---"Object > deleted from database" 609ms (15:04:56.488) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1214239173]: ---"Object > deleted from database" 580ms (15:04:56.493) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[783574743]: ---"Object > deleted from database" 584ms (15:04:56.498) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1600294098]: ---"Object > deleted from database" 595ms (15:04:56.502) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[985792831]: ---"Object > deleted from database" 620ms (15:04:56.506) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1107874578]: ---"Object > deleted from database" 634ms (15:04:56.510) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[406458206]: ---"Object > deleted from database" 616ms (15:04:56.515) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[654409944]: ---"Object > deleted from database" 652ms (15:04:56.519) > Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[2001160119]: ---"Object > deleted from database" 631ms (15:04:56.523) > Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" > level=info msg="Configuring sqlite3 database connection pooling: > maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s" > Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" > level=info msg="Configuring database table schema and indexes, this > may take a moment..." > Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" > level=info msg="Configuring sqlite3 database connection pooling: > maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s" > Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" > level=info msg="Configuring database table schema and indexes, this > may take a moment..." > Jul 07 16:14:21 chipstervm1 k3s[1046]: > time="2025-07-07T16:14:21+02:00" level=info msg="Configuring sqlite3 > database connection pooling: maxIdleConns=2, maxOpenConns=0, > connMaxLifetime=0s" > Jul 07 16:14:21 chipstervm1 k3s[1046]: > time="2025-07-07T16:14:21+02:00" level=info msg="Configuring database > table schema and indexes, this may take a moment..." > Jul 07 16:17:55 chipstervm1 k3s[4218]: > time="2025-07-07T16:17:55+02:00" level=info msg="Configuring sqlite3 > database connection pooling: maxIdleConns=2, maxOpenConns=0, > connMaxLifetime=0s" > Jul 07 16:17:55 chipstervm1 k3s[4218]: > time="2025-07-07T16:17:55+02:00" level=info msg="Configuring database > table schema and indexes, this may take a moment..." > Jul 22 10:58:21 chipstervm1 k3s[1032]: > time="2025-07-22T10:58:21+02:00" level=info msg="Configuring sqlite3 > database connection pooling: maxIdleConns=2, maxOpenConns=0, > connMaxLifetime=0s" > Jul 22 10:58:21 chipstervm1 k3s[1032]: > time="2025-07-22T10:58:21+02:00" level=info msg="Configuring database > table schema and indexes, this may take a moment..." > Jul 22 13:18:00 chipstervm1 k3s[11626]: > time="2025-07-22T13:18:00+02:00" level=info msg="Configuring sqlite3 > database connection pooling: maxIdleConns=2, maxOpenConns=0, > connMaxLifetime=0s" > Jul 22 13:18:00 chipstervm1 k3s[11626]: > time="2025-07-22T13:18:00+02:00" level=info msg="Configuring database > table schema and indexes, this may take a moment..." > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ sudo ls -l > /var/lib/rancher/k3s/server/db/ > [sudo] password for ubuntu: > total 12056 > drwx------ 2 root root 4096 Jul 22 13:18 etcd > -rw-r--r-- 1 root root 7655424 Jul 22 13:58 state.db > -rw-r--r-- 1 root root 32768 Jul 22 13:59 state.db-shm > -rw-r--r-- 1 root root 4647392 Jul 22 13:59 state.db-wal Am 22.07.2025 um 13:52 schrieb Chipster: > > Hi Oli, > > well, that’s certainly interesting. Let’s find out what’s the difference. > > -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
|
From: Chipster <chi...@cs...> - 2025-07-22 11:53:08
|
Hi Oli,
well, that’s certainly interesting. Let’s find out what’s the difference.
** Do you have the latest deployment scripts?
$ git log
commit 46016f41f46905bb7fc2390b5d188464fc6b27da (HEAD -> k3s, tag: v4.15.0, origin/k3s-ubuntu24, origin/k3s)
Author: Petri Klemela pet...@cs...<mailto:pet...@cs...>
Date: Wed May 14 09:41:59 2025 +0300
Fix typo
…
** Do we have the same K3s version?
$ k3s -v
k3s version v1.32.4+k3s1 (6b330558)
go version go1.23.6
** Does K3s have any extra namespaces that could hide something from us?
$ kubectl get namespace
NAME STATUS AGE
default Active 52m
kube-node-lease Active 52m
kube-public Active 52m
kube-system Active 52m
** Or IngressRoutes?
ubuntu@chipster-dev-86-50-168-180-1:~/git/chipster-openshift/k3s$ kubectl get ingressroute
NAME AGE
chipster 56m
** Or middlewares?
$ kubectl get middleware
NAME AGE
chipster-https-redirect 56m
chipster-stripprefix 56m
** Is the kubectl configured to control this this node and not some other remote server? Check that both commands show the same hostname:
$ kubectl get node
NAME STATUS ROLES AGE VERSION
<hostname> Ready control-plane,master 54m v1.32.4+k3s1
$ hostname
<hostname>
** Is K3s using SQLite as datastore?
$ journalctl -u k3s.service --no-pager | grep "database"
May 26 06:50:12 chipster-dev-86-50-168-180-1 k3s[3427]: time="2025-05-26T06:50:12Z" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
…
** The SQLite stores its data in /var/lib/rancher/k3s/server/db/ . Was it cleared when K3s was uninstalled?
sudo ls -l /var/lib/rancher/k3s/server/db/
total 30736
drwx------ 2 root root 4096 Jul 22 10:44 etcd
-rw-r--r-- 1 root root 19906560 Jul 22 11:46 state.db
-rw-r--r-- 1 root root 32768 Jul 22 11:48 state.db-shm
-rw-r--r-- 1 root root 11519552 Jul 22 11:48 state.db-wal
Best regards,
Petri / Chipster Team
--
Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...
From: Oliver Heil <o....@dk...>
Date: Tuesday, 22. July 2025 at 14.25
To: chi...@li... <chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
Hi Petri,
I did as you suggested (I hope you believe me), but the result stays the same:
At this point:
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash --set host=172.XX.26.XXX
Error: INSTALLATION FAILED: unable to build kubernetes objects from release manifest: [resource mapping not found for name: "chipster" namespace: "" from "": no matches for kind "IngressRoute" in version "traefik.containo.us/v1alpha1"
ensure CRDs are installed first, resource mapping not found for name: "chipster-stripprefix" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1"
ensure CRDs are installed first, resource mapping not found for name: "chipster-https-redirect" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1"
ensure CRDs are installed first]
Oli
Am 22.07.2025 um 13:03 schrieb Chipster:
Hi Oli,
sorry, you had shown already in the first message that you have deleted all Kubernetes secrets.
I’m not sure where the K3s still finds those old definitions. Anyway, if nothing needs to be saved, would it be easiest just to uninstall K3s (https://docs.k3s.io/installation/uninstall):
/usr/local/bin/k3s-uninstall.sh
Then reinstall K3s: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/prerequisites.md#install-k3s-helm-and-other-utils
And Chipster: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#deploy
Best regards,
Petri / Chipster Team
--
Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...<mailto:chi...@cs...>
From: Oliver Heil <o....@dk...><mailto:o....@dk...>
Date: Tuesday, 22. July 2025 at 12.29
To: chi...@li...<mailto:chi...@li...> <chi...@li...><mailto:chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
--
Oliver Heil (er/ihm,he/him)
Microarray Core Facility
Bioinformatics
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
o....@dk...<mailto:o....@dk...>
Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/>
www.dkfz.de<http://www.dkfz.de>
[Research for a Life without Cancer]
Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy>
Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja>
|
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From: Oliver H. <o....@dk...> - 2025-07-22 11:25:39
|
Hi Petri, I did as you suggested (I hope you believe me), but the result stays the same: At this point: > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash > --set host=172.XX.26.XXX > Error: INSTALLATION FAILED: unable to build kubernetes objects from > release manifest: [resource mapping not found for name: "chipster" > namespace: "" from "": no matches for kind "IngressRoute" in version > "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for name: > "chipster-stripprefix" namespace: "" from "": no matches for kind > "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for name: > "chipster-https-redirect" namespace: "" from "": no matches for kind > "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first] Oli Am 22.07.2025 um 13:03 schrieb Chipster: > > Hi Oli, > > sorry, you had shown already in the first message that you have > deleted all Kubernetes secrets. > > I’m not sure where the K3s still finds those old definitions. Anyway, > if nothing needs to be saved, would it be easiest just to uninstall > K3s (https://docs.k3s.io/installation/uninstall): > > /usr/local/bin/k3s-uninstall.sh > > Then reinstall K3s: > https://github.com/chipster/chipster-openshift/blob/k3s/k3s/prerequisites.md#install-k3s-helm-and-other-utils > > And Chipster: > https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#deploy > > Best regards, > > Petri / Chipster Team > > -- > > Petri Klemelä > > Chipster Team, CSC – IT Center for Science > > chi...@cs... > > *From: *Oliver Heil <o....@dk...> > *Date: *Tuesday, 22. July 2025 at 12.29 > *To: *chi...@li... > <chi...@li...> > *Subject: *Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 > updates in Chipster > > -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
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From: Chipster <chi...@cs...> - 2025-07-22 11:03:27
|
Hi Oli, sorry, you had shown already in the first message that you have deleted all Kubernetes secrets. I’m not sure where the K3s still finds those old definitions. Anyway, if nothing needs to be saved, would it be easiest just to uninstall K3s (https://docs.k3s.io/installation/uninstall): /usr/local/bin/k3s-uninstall.sh Then reinstall K3s: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/prerequisites.md#install-k3s-helm-and-other-utils And Chipster: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#deploy Best regards, Petri / Chipster Team -- Petri Klemelä Chipster Team, CSC – IT Center for Science chi...@cs... From: Oliver Heil <o....@dk...> Date: Tuesday, 22. July 2025 at 12.29 To: chi...@li... <chi...@li...> Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster Hi Petri, I followed the procedure already. I did it now again, with the only difference, that I upgraded the servers Ubuntu as usual, because since then, 18 more updates have been waiting. Ok, after doing it again I am now at this point: ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f ~/values.yaml Error: INSTALLATION FAILED: unable to build kubernetes objects from release manifest: [resource mapping not found for name: "chipster" namespace: "" from "": no matches for kind "IngressRoute" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-stripprefix" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-https-redirect" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first] Before that I did the bash pull-images.bash and it finished without any problems. And now ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret NAME TYPE DATA AGE passwords Opaque 1 14d which looks good. Best regards, Oli PS: there is nothing on the server which needs to be saved! Am 22.07.2025 um 06:53 schrieb Chipster: Hi Oli, unfortunately your error message looks a lot like the errors that I got when I tried to update the K3s before uninstalling Chipster. Luckily at least the update of the first server went through, so you have at least one working server. Does this second server store any analysis sessions that shouldn’t be lost? If it does, please do not make any further changes before we have verified where those are stored and how we can do this as safely as possible without losing them. If you are not too worried about losing the data stored on the server, then I would start by trying to delete the Helm releases like shown in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#recovering-from-failed-k3s-v1324-update . Best regards, Petri / Chipster Team -- Petri Klemelä Chipster Team, CSC – IT Center for Science chi...@cs...<mailto:chi...@cs...> From: Oliver Heil <o....@dk...><mailto:o....@dk...> Date: Monday, 7. July 2025 at 19.09 To: chi...@li...<mailto:chi...@li...> <chi...@li...><mailto:chi...@li...> Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster Dear Petri, I updated one server successfully, but the second one did not well. I am stuck here: ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f ~/values.yaml Error: INSTALLATION FAILED: unable to build kubernetes objects from release manifest: [resource mapping not found for name: "chipster" namespace: "" from "": no matches for kind "IngressRoute" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-stripprefix" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-https-redirect" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first] but ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret NAME TYPE DATA AGE passwords Opaque 1 37m I did already kubectl delete secret passwords but this did not resolve the issue. Of course I did helm uninstall chipster at first but yet I run into above known issue anyways. What can I do ? Best regards, Oli -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk...<mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/> www.dkfz.de<http://www.dkfz.de> [Research for a Life without Cancer] Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy> Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja> |
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From: Oliver H. <o....@dk...> - 2025-07-22 09:29:09
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Hi Petri, I followed the procedure already. I did it now again, with the only difference, that I upgraded the servers Ubuntu as usual, because since then, 18 more updates have been waiting. Ok, after doing it again I am now at this point: > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f > ~/values.yaml > Error: INSTALLATION FAILED: unable to build kubernetes objects from > release manifest: [resource mapping not found for name: "chipster" > namespace: "" from "": no matches for kind "IngressRoute" in version > "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for name: > "chipster-stripprefix" namespace: "" from "": no matches for kind > "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for name: > "chipster-https-redirect" namespace: "" from "": no matches for kind > "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first] Before that I did the > bash pull-images.bash and it finished without any problems. And now > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret > NAME TYPE DATA AGE > passwords Opaque 1 14d which looks good. Best regards, Oli PS: there is nothing on the server which needs to be saved! Am 22.07.2025 um 06:53 schrieb Chipster: > > Hi Oli, > > unfortunately your error message looks a lot like the errors that I > got when I tried to update the K3s before uninstalling Chipster. > Luckily at least the update of the first server went through, so you > have at least one working server. > > Does this second server store any analysis sessions that shouldn’t be > lost? If it does, please do not make any further changes before we > have verified where those are stored and how we can do this as safely > as possible without losing them. > > If you are not too worried about losing the data stored on the server, > then I would start by trying to delete the Helm releases like shown in > https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#recovering-from-failed-k3s-v1324-update > . > > Best regards, > > Petri / Chipster Team > > -- > > Petri Klemelä > > Chipster Team, CSC – IT Center for Science > > chi...@cs... > > *From: *Oliver Heil <o....@dk...> > *Date: *Monday, 7. July 2025 at 19.09 > *To: *chi...@li... > <chi...@li...> > *Subject: *Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 > updates in Chipster > > Dear Petri, > > I updated one server successfully, but the second one did not well. I > am stuck here: > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash > -f ~/values.yaml > Error: INSTALLATION FAILED: unable to build kubernetes objects > from release manifest: [resource mapping not found for name: > "chipster" namespace: "" from "": no matches for kind > "IngressRoute" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for > name: "chipster-stripprefix" namespace: "" from "": no matches for > kind "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for > name: "chipster-https-redirect" namespace: "" from "": no matches > for kind "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first] > > but > > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret > NAME TYPE DATA AGE > passwords Opaque 1 37m > > I did already > > kubectl delete secret passwords > > but this did not resolve the issue. > > Of course I did > > helm uninstall chipster > > at first but yet I run into above known issue anyways. > > What can I do ? > > Best regards, > > Oli > -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
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From: Chipster <chi...@cs...> - 2025-07-22 04:53:29
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Hi Oli, unfortunately your error message looks a lot like the errors that I got when I tried to update the K3s before uninstalling Chipster. Luckily at least the update of the first server went through, so you have at least one working server. Does this second server store any analysis sessions that shouldn’t be lost? If it does, please do not make any further changes before we have verified where those are stored and how we can do this as safely as possible without losing them. If you are not too worried about losing the data stored on the server, then I would start by trying to delete the Helm releases like shown in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#recovering-from-failed-k3s-v1324-update . Best regards, Petri / Chipster Team -- Petri Klemelä Chipster Team, CSC – IT Center for Science chi...@cs... From: Oliver Heil <o....@dk...> Date: Monday, 7. July 2025 at 19.09 To: chi...@li... <chi...@li...> Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster Dear Petri, I updated one server successfully, but the second one did not well. I am stuck here: ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f ~/values.yaml Error: INSTALLATION FAILED: unable to build kubernetes objects from release manifest: [resource mapping not found for name: "chipster" namespace: "" from "": no matches for kind "IngressRoute" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-stripprefix" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-https-redirect" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first] but ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret NAME TYPE DATA AGE passwords Opaque 1 37m I did already kubectl delete secret passwords but this did not resolve the issue. Of course I did helm uninstall chipster at first but yet I run into above known issue anyways. What can I do ? Best regards, Oli Am 15.05.2025 um 08:53 schrieb chipster--- via Chipster-tech: Hi all Chipster maintainers, until now main Chipster components have been running in Ubuntu 20.04, which will reach end of support at May 31 2025. Our installation instructions now start from Ubuntu 24.04. We have also prepared instructions for this update, but please read this whole message before starting. The Ubuntu update itself seems to be relatively easy. You can either install a new server, or update your current one. Old Chipster containers seem to work just fine in the new Ubuntu and vice versa, so it doesn't matter whether you update first the Ubuntu or the Chipster version. However, we used this oportunity to update also the K3s. Due to earlier update issues, we had it pinned down to version v1.26. We now updated it to v1.32. The new version doesn't seem to tolerate our old apiVersion definition "traefik.containo.us/v1alpha1" in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/helm/chipster/templates/ingress-route.yaml . We have updated the apiVersion definition in the current templates (Chipster v4.15.0), but the K3s still has problems with the old versions stored by Helm. If you install a new server, you will get Ubuntu 24.04, K3s v1.32 with our new templates, and everything will work just fine. But if you try to upgrade an old server, read our migration instructions carefully. The easiest solution that we found is to uninstall Chipster before the new K3s is installed. Without this the server ended up in a state where even downgrading of K3s didn't fix it. K3s v1.32 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-k3s-v1324 Ubuntu 24.04 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-ubuntu-2404 Chipster v4.15.0 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#updates Best regards, Petri / Chipster team _______________________________________________ Chipster-tech mailing list Chi...@li...<mailto:Chi...@li...> https://lists.sourceforge.net/lists/listinfo/chipster-tech -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk...<mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/> www.dkfz.de<http://www.dkfz.de> [Research for a Life without Cancer] Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy> Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja> |
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From: Oliver H. <o....@dk...> - 2025-07-10 10:00:45
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Hi Eija, Not urgent at all! It can easily wait until he is back and ready :-D (We have two Chipster installations and one is updated and fine) Thanks for asking and have a nice holiday, too (and soon) Oli Am 10.07.2025 um 11:40 schrieb Chipster via Chipster-tech: > Dear Oliver, > > Petri is currently on holidays, by he will be back on the 21st of > July. How critical is your situation? If your server is not > functioning at all, I will ask if he could help you during his holidays. > > Best, > Eija -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
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From: Chipster <chi...@cs...> - 2025-07-10 09:55:00
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Dear Oliver, Petri is currently on holidays, by he will be back on the 21st of July. How critical is your situation? If your server is not functioning at all, I will ask if he could help you during his holidays. Best, Eija ________________________________ From: Oliver Heil <o....@dk...> Sent: Monday, July 7, 2025 18:27 To: chi...@li... <chi...@li...> Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster Dear Petri, I updated one server successfully, but the second one did not well. I am stuck here: ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f ~/values.yaml Error: INSTALLATION FAILED: unable to build kubernetes objects from release manifest: [resource mapping not found for name: "chipster" namespace: "" from "": no matches for kind "IngressRoute" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-stripprefix" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first, resource mapping not found for name: "chipster-https-redirect" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1" ensure CRDs are installed first] but ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret NAME TYPE DATA AGE passwords Opaque 1 37m I did already kubectl delete secret passwords but this did not resolve the issue. Of course I did helm uninstall chipster at first but yet I run into above known issue anyways. What can I do ? Best regards, Oli Am 15.05.2025 um 08:53 schrieb chipster--- via Chipster-tech: Hi all Chipster maintainers, until now main Chipster components have been running in Ubuntu 20.04, which will reach end of support at May 31 2025. Our installation instructions now start from Ubuntu 24.04. We have also prepared instructions for this update, but please read this whole message before starting. The Ubuntu update itself seems to be relatively easy. You can either install a new server, or update your current one. Old Chipster containers seem to work just fine in the new Ubuntu and vice versa, so it doesn't matter whether you update first the Ubuntu or the Chipster version. However, we used this oportunity to update also the K3s. Due to earlier update issues, we had it pinned down to version v1.26. We now updated it to v1.32. The new version doesn't seem to tolerate our old apiVersion definition "traefik.containo.us/v1alpha1" in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/helm/chipster/templates/ingress-route.yaml . We have updated the apiVersion definition in the current templates (Chipster v4.15.0), but the K3s still has problems with the old versions stored by Helm. If you install a new server, you will get Ubuntu 24.04, K3s v1.32 with our new templates, and everything will work just fine. But if you try to upgrade an old server, read our migration instructions carefully. The easiest solution that we found is to uninstall Chipster before the new K3s is installed. Without this the server ended up in a state where even downgrading of K3s didn't fix it. K3s v1.32 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-k3s-v1324 Ubuntu 24.04 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-ubuntu-2404 Chipster v4.15.0 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#updates Best regards, Petri / Chipster team _______________________________________________ Chipster-tech mailing list Chi...@li...<mailto:Chi...@li...> https://lists.sourceforge.net/lists/listinfo/chipster-tech -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk...<mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/> www.dkfz.de<http://www.dkfz.de> [Research for a Life without Cancer] Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. For information on how we process personal data and our contact information, please see CSC's website: Privacy<https://csc.fi/en/privacy> Tämän sähköpostin tiedot voivat olla luottamuksellisia ja ne on tarkoitettu yksinomaan sen henkilön tai yhteisön käyttöön, jolle ne on osoitettu. Jos et ole viestissä tarkoitettu vastaanottaja, tuhoa viesti ja ilmoita asiasta välittömästi viestin lähettäjälle. Tietoja henkilötietojen ja yhteystietojen käsittelystä löydät CSC:n verkkosivuilta: Tietosuoja<https://csc.fi/tietosuoja> |
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From: Oliver H. <o....@dk...> - 2025-07-07 16:03:35
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Dear Petri, I updated one server successfully, but the second one did not well. I am stuck here: > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f > ~/values.yaml > Error: INSTALLATION FAILED: unable to build kubernetes objects from > release manifest: [resource mapping not found for name: "chipster" > namespace: "" from "": no matches for kind "IngressRoute" in version > "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for name: > "chipster-stripprefix" namespace: "" from "": no matches for kind > "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first, resource mapping not found for name: > "chipster-https-redirect" namespace: "" from "": no matches for kind > "Middleware" in version "traefik.containo.us/v1alpha1" > ensure CRDs are installed first] but > ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret > NAME TYPE DATA AGE > passwords Opaque 1 37m I did already > kubectl delete secret passwords but this did not resolve the issue. Of course I did > helm uninstall chipster at first but yet I run into above known issue anyways. What can I do ? Best regards, Oli Am 15.05.2025 um 08:53 schrieb chipster--- via Chipster-tech: > Hi all Chipster maintainers, > > until now main Chipster components have been running in Ubuntu 20.04, which will reach end of support at May 31 2025. Our installation instructions now start from Ubuntu 24.04. We have also prepared instructions for this update, but please read this whole message before starting. > > The Ubuntu update itself seems to be relatively easy. You can either install a new server, or update your current one. Old Chipster containers seem to work just fine in the new Ubuntu and vice versa, so it doesn't matter whether you update first the Ubuntu or the Chipster version. > > However, we used this oportunity to update also the K3s. Due to earlier update issues, we had it pinned down to version v1.26. We now updated it to v1.32. The new version doesn't seem to tolerate our old apiVersion definition "traefik.containo.us/v1alpha1" inhttps://github.com/chipster/chipster-openshift/blob/k3s/k3s/helm/chipster/templates/ingress-route.yaml . We have updated the apiVersion definition in the current templates (Chipster v4.15.0), but the K3s still has problems with the old versions stored by Helm. > > If you install a new server, you will get Ubuntu 24.04, K3s v1.32 with our new templates, and everything will work just fine. But if you try to upgrade an old server, read our migration instructions carefully. The easiest solution that we found is to uninstall Chipster before the new K3s is installed. Without this the server ended up in a state where even downgrading of K3s didn't fix it. > > K3s v1.32 update instructions: > > https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-k3s-v1324 > > Ubuntu 24.04 update instructions: > > https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-ubuntu-2404 > > Chipster v4.15.0 update instructions: > > https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#updates > > Best regards, > Petri / Chipster team > > > _______________________________________________ > Chipster-tech mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-tech -- Oliver Heil (er/ihm,he/him) Microarray Core Facility Bioinformatics German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany o....@dk... <mailto:o....@dk...> Support: www.dkfz.de/gpcf/support/ <https://www.dkfz.de/gpcf/support/> www.dkfz.de <http://www.dkfz.de> Research for a Life without Cancer Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 |
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From: <chi...@cs...> - 2025-05-15 06:54:09
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Hi all Chipster maintainers, until now main Chipster components have been running in Ubuntu 20.04, which will reach end of support at May 31 2025. Our installation instructions now start from Ubuntu 24.04. We have also prepared instructions for this update, but please read this whole message before starting. The Ubuntu update itself seems to be relatively easy. You can either install a new server, or update your current one. Old Chipster containers seem to work just fine in the new Ubuntu and vice versa, so it doesn't matter whether you update first the Ubuntu or the Chipster version. However, we used this oportunity to update also the K3s. Due to earlier update issues, we had it pinned down to version v1.26. We now updated it to v1.32. The new version doesn't seem to tolerate our old apiVersion definition "traefik.containo.us/v1alpha1" in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/helm/chipster/templates/ingress-route.yaml . We have updated the apiVersion definition in the current templates (Chipster v4.15.0), but the K3s still has problems with the old versions stored by Helm. If you install a new server, you will get Ubuntu 24.04, K3s v1.32 with our new templates, and everything will work just fine. But if you try to upgrade an old server, read our migration instructions carefully. The easiest solution that we found is to uninstall Chipster before the new K3s is installed. Without this the server ended up in a state where even downgrading of K3s didn't fix it. K3s v1.32 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-k3s-v1324 Ubuntu 24.04 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-ubuntu-2404 Chipster v4.15.0 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#updates Best regards, Petri / Chipster team |
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From: <chi...@cs...> - 2025-04-23 07:31:13
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Hi Yota, I'm happy to hear about your plans to setup your own Chipster server. When you setup your own server, you can create as many Chipster accounts on your server as you want, and you don't need any user account from us. Technically it's possible to run Chipster server on a laptop, but usually this is done only when developing the Chipster software. Server softwares often have problems to recover after the laptop changes network connection or after the laptop wakes up from the sleep mode. So a separate server is probably easier way forward. The server installation instructions are in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md . By the way, the operating system in the current server setup is Ubuntu 20.04, which is reaching its end of updates soon. I'll change it to Ubuntu 24.04, but it will take a couple of weeks. I don't expect this to change almost anything in Chipster, so the current version is perfectly fine for practicing the installation and for your testing phase. The upcoming updated version should be practically identical. I will send more information about the update version here on the chipster-tech email list when it's ready. Let us know if you have more questions about the server setup! Best regards, Petri / Chipster team ----- Original Message ----- From: "Kolypetri, Panagiota,Ph.D." <pko...@bw...> To: "chipster-tech" <chi...@li...> Sent: Tuesday, 22 April, 2025 18:01:39 Subject: [Chipster-tech] Question about Chipster installation Hello, I hope you are doing well. Recently, I attended two online tutorials on using Chipster for bulk RNAseq and single-cell RNAseq data analysis. I am interested in installing and trying out my data analysis using Chipster. Our lab is part of Brigham and Women's Hospital, Boston, USA. I talked to my PI, and he agreed with me on setting up the software and trying it out. Currently, we have a biostatistician in the lab, but he is always very busy. I checked your website, and I need to create a user account and do a local server installation. My question for you is the following. Since I am in a testing phase, can I use a personal laptop as a local server, or should I use a BWH computer as a local server, or does it make no difference? I am asking because, depending on your answer, I will have to contact the right person to help me with the server installation. Thank you in advance for your time and help. Best regards, Yota Panagiota Kolypetri, PhD Instructor of Neurology, Harvard Medical School Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital 60 Fenwood Road, BTM 10032 Boston, MA, 02115 Tel: 617-525-5327 Email: pko...@bw... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech |
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From: Kolypetri, Panagiota,Ph.D. <pko...@bw...> - 2025-04-22 15:17:47
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Hello,
I hope you are doing well. Recently, I attended two online tutorials on using Chipster for bulk RNAseq and single-cell RNAseq data analysis.
I am interested in installing and trying out my data analysis using Chipster. Our lab is part of Brigham and Women's Hospital, Boston, USA. I talked to my PI, and he agreed with me on setting up the software and trying it out. Currently, we have a biostatistician in the lab, but he is always very busy.
I checked your website, and I need to create a user account and do a local server installation. My question for you is the following. Since I am in a testing phase, can I use a personal laptop as a local server, or should I use a BWH computer as a local server, or does it make no difference? I am asking because, depending on your answer, I will have to contact the right person to help me with the server installation.
Thank you in advance for your time and help.
Best regards,
Yota
Panagiota Kolypetri, PhD
Instructor of Neurology, Harvard Medical School
Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital
60 Fenwood Road, BTM 10032
Boston, MA, 02115
Tel: 617-525-5327
Email: pko...@bw...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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From: <chi...@cs...> - 2024-12-10 07:54:35
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Hi Regan, happy to hear that it works! Best regards, Petri ----- Original Message ----- From: "Regan Cannell via Chipster-tech" <chi...@li...> To: "chipster-tech" <chi...@li...> Cc: "regan cannell" <reg...@wi...> Sent: Friday, 6 December, 2024 10:04:17 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi, Petri I've got good news: all the tools for Chipster-4.9.0 have been successfully installed. Thank you very much for your assistance. Kind regards Regan Mr Regan Cannell Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB) [cid:ima...@za...] E: reg...@wi... T: +27 117176636 <tel:+27%20117176636> W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/> [cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a0QLVG8xVcCQdNK> [cid:ima...@za...] [cid:ima...@za...] SBIMB First Floor, Office 104 The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa [cid:ima...@za...] From: Regan Cannell <reg...@wi...> Sent: 05 December 2024 16:16 To: chi...@li... <chi...@li...> Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Dear Petri Thank you very much. Yes, I am indeed missing several tools. That is probably the root cause of my problem. I am going to download all the tools and then install them. (It might take a while). I will let you know if it all works out. Thanks again for your assistance. Kind regards Regan From: chi...@cs... <chi...@cs...> Sent: 05 December 2024 15:36 To: chipster-tech <chi...@li...> Cc: Regan Cannell <reg...@wi...> Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi Regan, thanks for sending the additional details in the private message to chi...@cs.... I'll continue here on the public email list so that others can follow. Have you perhaps downloaded your tools-bin before 2024-09-27? Back then we noticed that the object list in https://a3s.fi/swift/v1/AUTH_chipcld/chipster-tools-bin/ shows only first about 1000 objects and therefore the old tools-bin download instructions didn't find all the parts of the tools-bin 4.9.0 (see https://sourceforge.net/p/chipster/mailman/message/58822037/ ). Probably the easiest way to verify this is to check the number of files and the total size of your tools-bin directory: $ cd /mnt/tools-bin $ find chipster-4.9.0 | wc -l 386231 $ du -sh chipster-4.9.0 406G chipster-4.9.0 Both of these commands may take several minutes. These numbers were from my development machine, so there can be small differences, but the tools-bin should have about 390k files and the size should be about 410G . If your numbers are smaller, then your previous tools-bin download was only partial because of this bug. This has been fixed in the current instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/tools-bin-host-mount.md . So if you follow the instructions now and download the tools-bin again, you should get all parts of it, including the CellBender. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: "chipster-tech" <chi...@li...> Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 13:33:59 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Sorry, the correct tools-bin version should have been chipster-4.9.0. There was one extra character 'v'. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 12:56:02 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi Regan, thanks for the detailed error report. which version of the tools-bin package do you have at the moment? Our latest tools-bin version chipster-v4.9.0 (released a year ago) includes CellBender already. Would it be possible for you to download that? This would probably be the easiest solution, because then Chipster tool scripts would find the correct versions of all analysis tools in correct paths. If that is not an option, I can have a closer look why Chipster doesn't find your installation of the CellBender. Best regards, Petri ----- Original Message ----- From: "Regan Cannell via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "Regan Cannell" <reg...@wi...> Sent: Wednesday, 4 December, 2024 14:43:57 Subject: [Chipster-tech] Installing Cellbender in Chipster To whom it may concern My client has requested to use the tool called cellbender. However, this tool is not installed in the Chipster tools-bin directory, which I have mounted at /mnt/data/chipster/tools-bin/. The documentation states that for any tool that requires R-4.2.3, we need to build the Docker image locally and then add the necessary configurations to the values.yaml file. This is what I have added to my values.yaml file: ```yaml deployments: toolbox: password: XXXXXXXXXXXXXXXXXXXXXXXXX configs: toolbox-runtime-command-R-4.2.3-cellbender: /opt/chipster/tools/R-4.2.3/bin/R toolbox-runtime-image-R-4.2.3-cellbender: comp-r-4-2-3-cellbender toolbox-runtime-tools-bin-path-R-4.2.3-cellbender: tools-bin ``` The name of the tool in the Chipster interface is Single-cell RNA-seq (Seurat v5, new) / Seurat v5 -Remove background contamination with CellBender, and I've attached a screenshot of the error logs. The logs state, "sh: 1: /opt/chipster/tools-bin/python-3.7.17/bin/cellbender: not found". My first plan of action was to manually install the cellbender package into the tools-bin directory. I used the following script: ```bash wget https://www.python.org/ftp/python/3.7.17/Python-3.7.17.tgz tar -xzf Python-3.7.17.tgz cd Python-3.7.17 ./configure --prefix=/opt/chipster/tools-bin/python-3.7.17 make make install /opt/chipster/tools-bin/python-3.7.17/bin/python3 --version cd /opt/chipster/tools-bin/python-3.7.17 bin/pip3 install cellbender==v0.3.0 bin/cellbender --version ``` I was able to install it, but Chipster does not recognise it. Please assist me in figuring out what I did wrong. I'd greatly appreciate it. Thank you. Kind regards Regan Mr Regan Cannell Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB) [cid:ima...@za...] E: reg...@wi... T: +27 117176636 <tel:+27%20117176636> W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/><http://www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/>> [cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a08k9G8krRtAjPs> [cid:ima...@za...] [cid:ima...@za...] SBIMB First Floor, Office 104 The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa [cid:ima...@za...] This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech |
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From: Regan C. <reg...@wi...> - 2024-12-06 08:04:48
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Hi, Petri I've got good news: all the tools for Chipster-4.9.0 have been successfully installed. Thank you very much for your assistance. Kind regards Regan Mr Regan Cannell Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB) [cid:ima...@za...] E: reg...@wi... T: +27 117176636 <tel:+27%20117176636> W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/> [cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a0QLVG8xVcCQdNK> [cid:ima...@za...] [cid:ima...@za...] SBIMB First Floor, Office 104 The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa [cid:ima...@za...] From: Regan Cannell <reg...@wi...> Sent: 05 December 2024 16:16 To: chi...@li... <chi...@li...> Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Dear Petri Thank you very much. Yes, I am indeed missing several tools. That is probably the root cause of my problem. I am going to download all the tools and then install them. (It might take a while). I will let you know if it all works out. Thanks again for your assistance. Kind regards Regan From: chi...@cs... <chi...@cs...> Sent: 05 December 2024 15:36 To: chipster-tech <chi...@li...> Cc: Regan Cannell <reg...@wi...> Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi Regan, thanks for sending the additional details in the private message to chi...@cs.... I'll continue here on the public email list so that others can follow. Have you perhaps downloaded your tools-bin before 2024-09-27? Back then we noticed that the object list in https://a3s.fi/swift/v1/AUTH_chipcld/chipster-tools-bin/ shows only first about 1000 objects and therefore the old tools-bin download instructions didn't find all the parts of the tools-bin 4.9.0 (see https://sourceforge.net/p/chipster/mailman/message/58822037/ ). Probably the easiest way to verify this is to check the number of files and the total size of your tools-bin directory: $ cd /mnt/tools-bin $ find chipster-4.9.0 | wc -l 386231 $ du -sh chipster-4.9.0 406G chipster-4.9.0 Both of these commands may take several minutes. These numbers were from my development machine, so there can be small differences, but the tools-bin should have about 390k files and the size should be about 410G . If your numbers are smaller, then your previous tools-bin download was only partial because of this bug. This has been fixed in the current instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/tools-bin-host-mount.md . So if you follow the instructions now and download the tools-bin again, you should get all parts of it, including the CellBender. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: "chipster-tech" <chi...@li...> Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 13:33:59 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Sorry, the correct tools-bin version should have been chipster-4.9.0. There was one extra character 'v'. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 12:56:02 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi Regan, thanks for the detailed error report. which version of the tools-bin package do you have at the moment? Our latest tools-bin version chipster-v4.9.0 (released a year ago) includes CellBender already. Would it be possible for you to download that? This would probably be the easiest solution, because then Chipster tool scripts would find the correct versions of all analysis tools in correct paths. If that is not an option, I can have a closer look why Chipster doesn't find your installation of the CellBender. Best regards, Petri ----- Original Message ----- From: "Regan Cannell via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "Regan Cannell" <reg...@wi...> Sent: Wednesday, 4 December, 2024 14:43:57 Subject: [Chipster-tech] Installing Cellbender in Chipster To whom it may concern My client has requested to use the tool called cellbender. However, this tool is not installed in the Chipster tools-bin directory, which I have mounted at /mnt/data/chipster/tools-bin/. The documentation states that for any tool that requires R-4.2.3, we need to build the Docker image locally and then add the necessary configurations to the values.yaml file. This is what I have added to my values.yaml file: ```yaml deployments: toolbox: password: XXXXXXXXXXXXXXXXXXXXXXXXX configs: toolbox-runtime-command-R-4.2.3-cellbender: /opt/chipster/tools/R-4.2.3/bin/R toolbox-runtime-image-R-4.2.3-cellbender: comp-r-4-2-3-cellbender toolbox-runtime-tools-bin-path-R-4.2.3-cellbender: tools-bin ``` The name of the tool in the Chipster interface is Single-cell RNA-seq (Seurat v5, new) / Seurat v5 -Remove background contamination with CellBender, and I've attached a screenshot of the error logs. The logs state, "sh: 1: /opt/chipster/tools-bin/python-3.7.17/bin/cellbender: not found". My first plan of action was to manually install the cellbender package into the tools-bin directory. I used the following script: ```bash wget https://www.python.org/ftp/python/3.7.17/Python-3.7.17.tgz tar -xzf Python-3.7.17.tgz cd Python-3.7.17 ./configure --prefix=/opt/chipster/tools-bin/python-3.7.17 make make install /opt/chipster/tools-bin/python-3.7.17/bin/python3 --version cd /opt/chipster/tools-bin/python-3.7.17 bin/pip3 install cellbender==v0.3.0 bin/cellbender --version ``` I was able to install it, but Chipster does not recognise it. Please assist me in figuring out what I did wrong. I'd greatly appreciate it. Thank you. Kind regards Regan Mr Regan Cannell Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB) [cid:ima...@za...] E: reg...@wi... T: +27 117176636 <tel:+27%20117176636> W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/><http://www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/>> [cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a08k9G8krRtAjPs> [cid:ima...@za...] [cid:ima...@za...] SBIMB First Floor, Office 104 The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa [cid:ima...@za...] This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. |
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From: Regan C. <reg...@wi...> - 2024-12-05 14:31:02
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Dear Petri Thank you very much. Yes, I am indeed missing several tools. That is probably the root cause of my problem. I am going to download all the tools and then install them. (It might take a while). I will let you know if it all works out. Thanks again for your assistance. Kind regards Regan Mr Regan Cannell Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB) [cid:ima...@za...] E: reg...@wi... T: +27 117176636 <tel:+27%20117176636> W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/> [cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a0BQZfgs7LqyuJC> [cid:ima...@za...] [cid:ima...@za...] SBIMB First Floor, Office 104 The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa [cid:ima...@za...] From: chi...@cs... <chi...@cs...> Sent: 05 December 2024 15:36 To: chipster-tech <chi...@li...> Cc: Regan Cannell <reg...@wi...> Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi Regan, thanks for sending the additional details in the private message to chi...@cs.... I'll continue here on the public email list so that others can follow. Have you perhaps downloaded your tools-bin before 2024-09-27? Back then we noticed that the object list in https://a3s.fi/swift/v1/AUTH_chipcld/chipster-tools-bin/ shows only first about 1000 objects and therefore the old tools-bin download instructions didn't find all the parts of the tools-bin 4.9.0 (see https://sourceforge.net/p/chipster/mailman/message/58822037/ ). Probably the easiest way to verify this is to check the number of files and the total size of your tools-bin directory: $ cd /mnt/tools-bin $ find chipster-4.9.0 | wc -l 386231 $ du -sh chipster-4.9.0 406G chipster-4.9.0 Both of these commands may take several minutes. These numbers were from my development machine, so there can be small differences, but the tools-bin should have about 390k files and the size should be about 410G . If your numbers are smaller, then your previous tools-bin download was only partial because of this bug. This has been fixed in the current instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/tools-bin-host-mount.md . So if you follow the instructions now and download the tools-bin again, you should get all parts of it, including the CellBender. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: "chipster-tech" <chi...@li...> Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 13:33:59 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Sorry, the correct tools-bin version should have been chipster-4.9.0. There was one extra character 'v'. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 12:56:02 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi Regan, thanks for the detailed error report. which version of the tools-bin package do you have at the moment? Our latest tools-bin version chipster-v4.9.0 (released a year ago) includes CellBender already. Would it be possible for you to download that? This would probably be the easiest solution, because then Chipster tool scripts would find the correct versions of all analysis tools in correct paths. If that is not an option, I can have a closer look why Chipster doesn't find your installation of the CellBender. Best regards, Petri ----- Original Message ----- From: "Regan Cannell via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "Regan Cannell" <reg...@wi...> Sent: Wednesday, 4 December, 2024 14:43:57 Subject: [Chipster-tech] Installing Cellbender in Chipster To whom it may concern My client has requested to use the tool called cellbender. However, this tool is not installed in the Chipster tools-bin directory, which I have mounted at /mnt/data/chipster/tools-bin/. The documentation states that for any tool that requires R-4.2.3, we need to build the Docker image locally and then add the necessary configurations to the values.yaml file. This is what I have added to my values.yaml file: ```yaml deployments: toolbox: password: XXXXXXXXXXXXXXXXXXXXXXXXX configs: toolbox-runtime-command-R-4.2.3-cellbender: /opt/chipster/tools/R-4.2.3/bin/R toolbox-runtime-image-R-4.2.3-cellbender: comp-r-4-2-3-cellbender toolbox-runtime-tools-bin-path-R-4.2.3-cellbender: tools-bin ``` The name of the tool in the Chipster interface is Single-cell RNA-seq (Seurat v5, new) / Seurat v5 -Remove background contamination with CellBender, and I've attached a screenshot of the error logs. The logs state, "sh: 1: /opt/chipster/tools-bin/python-3.7.17/bin/cellbender: not found". My first plan of action was to manually install the cellbender package into the tools-bin directory. I used the following script: ```bash wget https://www.python.org/ftp/python/3.7.17/Python-3.7.17.tgz tar -xzf Python-3.7.17.tgz cd Python-3.7.17 ./configure --prefix=/opt/chipster/tools-bin/python-3.7.17 make make install /opt/chipster/tools-bin/python-3.7.17/bin/python3 --version cd /opt/chipster/tools-bin/python-3.7.17 bin/pip3 install cellbender==v0.3.0 bin/cellbender --version ``` I was able to install it, but Chipster does not recognise it. Please assist me in figuring out what I did wrong. I'd greatly appreciate it. Thank you. Kind regards Regan Mr Regan Cannell Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB) [cid:ima...@za...] E: reg...@wi... T: +27 117176636 <tel:+27%20117176636> W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/><http://www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/>> [cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a08k9G8krRtAjPs> [cid:ima...@za...] [cid:ima...@za...] SBIMB First Floor, Office 104 The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa [cid:ima...@za...] This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. |
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From: <chi...@cs...> - 2024-12-05 13:36:26
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Hi Regan, thanks for sending the additional details in the private message to chi...@cs.... I'll continue here on the public email list so that others can follow. Have you perhaps downloaded your tools-bin before 2024-09-27? Back then we noticed that the object list in https://a3s.fi/swift/v1/AUTH_chipcld/chipster-tools-bin/ shows only first about 1000 objects and therefore the old tools-bin download instructions didn't find all the parts of the tools-bin 4.9.0 (see https://sourceforge.net/p/chipster/mailman/message/58822037/ ). Probably the easiest way to verify this is to check the number of files and the total size of your tools-bin directory: $ cd /mnt/tools-bin $ find chipster-4.9.0 | wc -l 386231 $ du -sh chipster-4.9.0 406G chipster-4.9.0 Both of these commands may take several minutes. These numbers were from my development machine, so there can be small differences, but the tools-bin should have about 390k files and the size should be about 410G . If your numbers are smaller, then your previous tools-bin download was only partial because of this bug. This has been fixed in the current instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/tools-bin-host-mount.md . So if you follow the instructions now and download the tools-bin again, you should get all parts of it, including the CellBender. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: "chipster-tech" <chi...@li...> Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 13:33:59 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Sorry, the correct tools-bin version should have been chipster-4.9.0. There was one extra character 'v'. Best regards, Petri ----- Original Message ----- From: "chipster--- via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "chipster" <chi...@cs...> Sent: Thursday, 5 December, 2024 12:56:02 Subject: Re: [Chipster-tech] Installing Cellbender in Chipster Hi Regan, thanks for the detailed error report. which version of the tools-bin package do you have at the moment? Our latest tools-bin version chipster-v4.9.0 (released a year ago) includes CellBender already. Would it be possible for you to download that? This would probably be the easiest solution, because then Chipster tool scripts would find the correct versions of all analysis tools in correct paths. If that is not an option, I can have a closer look why Chipster doesn't find your installation of the CellBender. Best regards, Petri ----- Original Message ----- From: "Regan Cannell via Chipster-tech" <chi...@li...> To: chi...@li... Cc: "Regan Cannell" <reg...@wi...> Sent: Wednesday, 4 December, 2024 14:43:57 Subject: [Chipster-tech] Installing Cellbender in Chipster To whom it may concern My client has requested to use the tool called cellbender. However, this tool is not installed in the Chipster tools-bin directory, which I have mounted at /mnt/data/chipster/tools-bin/. The documentation states that for any tool that requires R-4.2.3, we need to build the Docker image locally and then add the necessary configurations to the values.yaml file. This is what I have added to my values.yaml file: ```yaml deployments: toolbox: password: XXXXXXXXXXXXXXXXXXXXXXXXX configs: toolbox-runtime-command-R-4.2.3-cellbender: /opt/chipster/tools/R-4.2.3/bin/R toolbox-runtime-image-R-4.2.3-cellbender: comp-r-4-2-3-cellbender toolbox-runtime-tools-bin-path-R-4.2.3-cellbender: tools-bin ``` The name of the tool in the Chipster interface is Single-cell RNA-seq (Seurat v5, new) / Seurat v5 -Remove background contamination with CellBender, and I've attached a screenshot of the error logs. The logs state, "sh: 1: /opt/chipster/tools-bin/python-3.7.17/bin/cellbender: not found". My first plan of action was to manually install the cellbender package into the tools-bin directory. I used the following script: ```bash wget https://www.python.org/ftp/python/3.7.17/Python-3.7.17.tgz tar -xzf Python-3.7.17.tgz cd Python-3.7.17 ./configure --prefix=/opt/chipster/tools-bin/python-3.7.17 make make install /opt/chipster/tools-bin/python-3.7.17/bin/python3 --version cd /opt/chipster/tools-bin/python-3.7.17 bin/pip3 install cellbender==v0.3.0 bin/cellbender --version ``` I was able to install it, but Chipster does not recognise it. Please assist me in figuring out what I did wrong. I'd greatly appreciate it. Thank you. Kind regards Regan Mr Regan Cannell Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB) [cid:ima...@za...] E: reg...@wi... T: +27 117176636 <tel:+27%20117176636> W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/> [cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a08k9G8krRtAjPs> [cid:ima...@za...] [cid:ima...@za...] SBIMB First Floor, Office 104 The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa [cid:ima...@za...] This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech _______________________________________________ Chipster-tech mailing list Chi...@li... https://lists.sourceforge.net/lists/listinfo/chipster-tech |
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From: <chi...@cs...> - 2024-12-05 11:34:15
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Sorry, the correct tools-bin version should have been chipster-4.9.0. There was one extra character 'v'.
Best regards,
Petri
----- Original Message -----
From: "chipster--- via Chipster-tech" <chi...@li...>
To: chi...@li...
Cc: "chipster" <chi...@cs...>
Sent: Thursday, 5 December, 2024 12:56:02
Subject: Re: [Chipster-tech] Installing Cellbender in Chipster
Hi Regan,
thanks for the detailed error report.
which version of the tools-bin package do you have at the moment? Our latest tools-bin version chipster-v4.9.0 (released a year ago) includes CellBender already. Would it be possible for you to download that? This would probably be the easiest solution, because then Chipster tool scripts would find the correct versions of all analysis tools in correct paths.
If that is not an option, I can have a closer look why Chipster doesn't find your installation of the CellBender.
Best regards,
Petri
----- Original Message -----
From: "Regan Cannell via Chipster-tech" <chi...@li...>
To: chi...@li...
Cc: "Regan Cannell" <reg...@wi...>
Sent: Wednesday, 4 December, 2024 14:43:57
Subject: [Chipster-tech] Installing Cellbender in Chipster
To whom it may concern
My client has requested to use the tool called cellbender. However, this tool is not installed in the Chipster tools-bin directory, which I have mounted at /mnt/data/chipster/tools-bin/.
The documentation states that for any tool that requires R-4.2.3, we need to build the Docker image locally and then add the necessary configurations to the values.yaml file. This is what I have added to my values.yaml file:
```yaml
deployments:
toolbox:
password: XXXXXXXXXXXXXXXXXXXXXXXXX
configs:
toolbox-runtime-command-R-4.2.3-cellbender: /opt/chipster/tools/R-4.2.3/bin/R
toolbox-runtime-image-R-4.2.3-cellbender: comp-r-4-2-3-cellbender
toolbox-runtime-tools-bin-path-R-4.2.3-cellbender: tools-bin
```
The name of the tool in the Chipster interface is
Single-cell RNA-seq (Seurat v5, new) / Seurat v5 -Remove background contamination with CellBender,
and I've attached a screenshot of the error logs.
The logs state, "sh: 1: /opt/chipster/tools-bin/python-3.7.17/bin/cellbender: not found". My first plan of action
was to manually install the cellbender package into the tools-bin directory. I used the following script:
```bash
wget https://www.python.org/ftp/python/3.7.17/Python-3.7.17.tgz
tar -xzf Python-3.7.17.tgz
cd Python-3.7.17
./configure --prefix=/opt/chipster/tools-bin/python-3.7.17
make
make install
/opt/chipster/tools-bin/python-3.7.17/bin/python3 --version
cd /opt/chipster/tools-bin/python-3.7.17
bin/pip3 install cellbender==v0.3.0
bin/cellbender --version
```
I was able to install it, but Chipster does not recognise it.
Please assist me in figuring out what I did wrong. I'd greatly appreciate it. Thank you.
Kind regards
Regan
Mr Regan Cannell
Software Developer at SBIMB | Sydney Brenner Institute for Molecular Bioscience (SBIMB)
[cid:ima...@za...]
E: reg...@wi...
T: +27 117176636 <tel:+27%20117176636>
W: www.wits.ac.za/research/sbimb/<https://www.wits.ac.za/research/sbimb/>
[cid:ima...@za...]<https://za01.rocketseed.cloud/rs/a08k9G8krRtAjPs>
[cid:ima...@za...]
[cid:ima...@za...]
SBIMB First Floor, Office 104
The Mount, 9 Jubilee Road, Parktown, Johannesburg, South Africa
[cid:ima...@za...]
This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.
_______________________________________________
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Chi...@li...
https://lists.sourceforge.net/lists/listinfo/chipster-tech
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Chi...@li...
https://lists.sourceforge.net/lists/listinfo/chipster-tech
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