Re: [Chipster-tech] [Extern] - Re: Microarray PCA analysis not starting

[Oliver H. <o....@dk...>]

Hi Petri,

> Or if you have your own git branch (check with 'git status'):
>
> cd ~/git/chipster-tools/
> git switch master
> git pull
> git switch <your-own-branch>
> git merge master
> bash reload.bash

This.

I have my own branch 'dkfz-tools' here
https://github.com/oheil/chipster-tools

I did as you said and it seems to be fine now.

I am now in sync with master on master and ahead 3 commits on dkfz-tools
Most changes in branch dkfz-tools I could make a PR, it's mainly this:

> phenodata <- read.table('phenodata.tsv', header=TRUE, sep='\t', 
> quote='', as.is=TRUE, check.names=FALSE, comment.char='')
instead of

> phenodata <- read.table("phenodata.tsv", header = TRUE, sep = "\t", 
> as.is = TRUE)

But there are also some changes, e.g. for special chip types, which you 
may not want.

Do you want me to do a PR from dkfz-tools now?
My guess is, that it wouldn't be merged right away but that we would go into
a few discussions, which is not a problem on my side. But if you say, it 
may take weeks
until we start a merge discussion I would say, ok, lets do it at some 
time in future...

Regards,

Oli


Am 08.09.2023 um 07:02 schrieb Chipster:
> Hi Oli,
>
> interesting. It looks like you still have the old tool scripts 
> somehow. Have you mounted the tool scripts from the host 
> (https://github.com/chipster/chipster-openshift/blob/master/k3s/tool-script-dev.md#mount-tool-scripts-from-the-host) 
> , i.e. something like this in your values.yaml?
>
>   tools:
>     hostPath: /opt/chipster/toolbox/tools
>
> In that case you would have to also update the tool scripts on your host:
>
> cd ~/git/chipster-tools/
> git pull
> bash reload.bash
>
> Unfortunately the reload script hasn't been very reliable. It should 
> print some logs. If the log timestamps are not from the current UTC 
> time, then the reload didn't happen. In that case, restart the whole 
> toolbox and wait for the old pod to disappear:
>
> kubectl rollout restart deployment/toolbox
> watch kubectl get pod
>
> Or if you have your own git branch (check with 'git status'):
>
> cd ~/git/chipster-tools/
> git switch master
> git pull
> git switch <your-own-branch>
> git merge master
> bash reload.bash
>
> If you haven't mounted the tools scripts from the host, then the tool 
> scripts should come directly from the toolbox container image and the 
> version tag should make sure you are running the latest version of it. 
> I guess we should then check how to toolbox deployment looks like:
>
> kubectl get deployment/toolbox -o yaml
>
> Best regards,
> Petri
>
-- 

Oliver Heil
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/>
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