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From: Jose M. de la R. T. <del...@gm...> - 2017-06-13 15:14:27
|
Hi David, I think that the SCIPION_TESTS is configurable, but we don't use that option very often. Could you try to provide the full absolute path? Anyway, I will recommend to download the test data in advance and allow users read-only access. Some of the datasets for the tests contains big files (needed for real EM tests) and you can end up with many copies of this test data per user. Where is the --paths options that you are asking about? On Tue, Jun 13, 2017 at 5:06 PM, Hoover , David (NIH/CIT) [E] < hoo...@he...> wrote: > Ah, you're right. Once I run the test, other users can run it as well. > > From my investigations, it seems that the tests directory should be > configurable. The files in $SCIPION_HOME have entries: > > config/scipion.conf:SCIPION_TESTS = data/tests > config/templates/scipion.template:SCIPION_TESTS = data/tests > > If I change these to something more generic, e.g. > > config/scipion.conf:SCIPION_TESTS = ~/data/tests > config/templates/scipion.template:SCIPION_TESTS = ~/data/tests > > This still fails. Is the SCIPION_TESTS variable actually configurable? > It seems that the path is hard-coded somewhere. > > One more question. What does the --paths option do? That didn't seem to > affect anything. > > David > > On Jun 13, 2017, at 10:49 AM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > > Hi David, > > It is not a silly question, I think that we should put it in a FAQ wiki > page. > > Scipion is designed so it can be used in multi-users environments, where > the administration install it and give just read and execution permission > to the users. > The problem with the tests is that the data is downloaded in > /path/to/scipion/data/tests, so the admin should download the the datasets > for the tests in advance. > In that way, the users can execute the test without the need to download > the dataset in that location. > > If you use the following command you can see the available datasets: > > scipion testdata --help (or --list) > > Hope this helps > Bests, > Jose Miguel > > On Tue, Jun 13, 2017 at 4:30 PM, Hoover , David (NIH/CIT) [E] < > hoo...@he...> wrote: > >> Hi, >> >> I'm new to Scipion, so I hope this is not a silly question. >> >> Can Scipion be used in a multiuser mode? That is, can an administrator >> install Scipion in a central, shared location, and have other users with >> only read permission to that central location run Scipion with input/output >> in their own local directories? >> >> So far, I can't figure out a way of doing this. Running the simple tests >> give error messages. For example, >> >> scipion tests model.test_mappers >> ... >> [ FAILED ] TestSqliteMapper.test_SqliteDb >> >> Traceback (most recent call last): >> File "/usr/local/apps/scipion/1.1/software/lib/python2.7/unittest/case.py", >> line 329, in run >> testMethod() >> File "/usr/local/apps/scipion/1.1/pyworkflow/tests/model/test_mappers.py", >> line 56, in test_SqliteDb >> db._createConnection(self.modelGoldSqlite, timeout=1000) >> File "/usr/local/apps/scipion/1.1/pyworkflow/mapper/sqlite_db.py", >> line 52, in _createConnection >> self.connection = sqlite.Connection(dbName, timeout, >> check_same_thread=False) >> OperationalError: unable to open database file >> >> Thanks, >> David Hoover >> HPC @ NIH >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > |
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From: Hoover , D. (NIH/C. [E] <hoo...@he...> - 2017-06-13 15:07:49
|
Ah, you're right. Once I run the test, other users can run it as well. From my investigations, it seems that the tests directory should be configurable. The files in $SCIPION_HOME have entries: config/scipion.conf:SCIPION_TESTS = data/tests config/templates/scipion.template:SCIPION_TESTS = data/tests If I change these to something more generic, e.g. config/scipion.conf:SCIPION_TESTS = ~/data/tests config/templates/scipion.template:SCIPION_TESTS = ~/data/tests This still fails. Is the SCIPION_TESTS variable actually configurable? It seems that the path is hard-coded somewhere. One more question. What does the --paths option do? That didn't seem to affect anything. David > On Jun 13, 2017, at 10:49 AM, Jose Miguel de la Rosa Trevin <del...@gm...> wrote: > > Hi David, > > It is not a silly question, I think that we should put it in a FAQ wiki page. > > Scipion is designed so it can be used in multi-users environments, where the administration install it and give just read and execution permission to the users. > The problem with the tests is that the data is downloaded in /path/to/scipion/data/tests, so the admin should download the the datasets for the tests in advance. > In that way, the users can execute the test without the need to download the dataset in that location. > > If you use the following command you can see the available datasets: > > scipion testdata --help (or --list) > > Hope this helps > Bests, > Jose Miguel > > On Tue, Jun 13, 2017 at 4:30 PM, Hoover , David (NIH/CIT) [E] <hoo...@he... <mailto:hoo...@he...>> wrote: > Hi, > > I'm new to Scipion, so I hope this is not a silly question. > > Can Scipion be used in a multiuser mode? That is, can an administrator install Scipion in a central, shared location, and have other users with only read permission to that central location run Scipion with input/output in their own local directories? > > So far, I can't figure out a way of doing this. Running the simple tests give error messages. For example, > > scipion tests model.test_mappers > ... > [ FAILED ] TestSqliteMapper.test_SqliteDb > > Traceback (most recent call last): > File "/usr/local/apps/scipion/1.1/software/lib/python2.7/unittest/case.py", line 329, in run > testMethod() > File "/usr/local/apps/scipion/1.1/pyworkflow/tests/model/test_mappers.py", line 56, in test_SqliteDb > db._createConnection(self.modelGoldSqlite, timeout=1000) > File "/usr/local/apps/scipion/1.1/pyworkflow/mapper/sqlite_db.py", line 52, in _createConnection > self.connection = sqlite.Connection(dbName, timeout, check_same_thread=False) > OperationalError: unable to open database file > > Thanks, > David Hoover > HPC @ NIH > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot> > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > |
|
From: Jose M. de la R. T. <del...@gm...> - 2017-06-13 14:49:36
|
Hi David, It is not a silly question, I think that we should put it in a FAQ wiki page. Scipion is designed so it can be used in multi-users environments, where the administration install it and give just read and execution permission to the users. The problem with the tests is that the data is downloaded in /path/to/scipion/data/tests, so the admin should download the the datasets for the tests in advance. In that way, the users can execute the test without the need to download the dataset in that location. If you use the following command you can see the available datasets: scipion testdata --help (or --list) Hope this helps Bests, Jose Miguel On Tue, Jun 13, 2017 at 4:30 PM, Hoover , David (NIH/CIT) [E] < hoo...@he...> wrote: > Hi, > > I'm new to Scipion, so I hope this is not a silly question. > > Can Scipion be used in a multiuser mode? That is, can an administrator > install Scipion in a central, shared location, and have other users with > only read permission to that central location run Scipion with input/output > in their own local directories? > > So far, I can't figure out a way of doing this. Running the simple tests > give error messages. For example, > > scipion tests model.test_mappers > ... > [ FAILED ] TestSqliteMapper.test_SqliteDb > > Traceback (most recent call last): > File "/usr/local/apps/scipion/1.1/software/lib/python2.7/unittest/case.py", > line 329, in run > testMethod() > File "/usr/local/apps/scipion/1.1/pyworkflow/tests/model/test_mappers.py", > line 56, in test_SqliteDb > db._createConnection(self.modelGoldSqlite, timeout=1000) > File "/usr/local/apps/scipion/1.1/pyworkflow/mapper/sqlite_db.py", line > 52, in _createConnection > self.connection = sqlite.Connection(dbName, timeout, > check_same_thread=False) > OperationalError: unable to open database file > > Thanks, > David Hoover > HPC @ NIH > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Hoover , D. (NIH/C. [E] <hoo...@he...> - 2017-06-13 14:36:42
|
Hi,
I'm new to Scipion, so I hope this is not a silly question.
Can Scipion be used in a multiuser mode? That is, can an administrator install Scipion in a central, shared location, and have other users with only read permission to that central location run Scipion with input/output in their own local directories?
So far, I can't figure out a way of doing this. Running the simple tests give error messages. For example,
scipion tests model.test_mappers
...
[ FAILED ] TestSqliteMapper.test_SqliteDb
Traceback (most recent call last):
File "/usr/local/apps/scipion/1.1/software/lib/python2.7/unittest/case.py", line 329, in run
testMethod()
File "/usr/local/apps/scipion/1.1/pyworkflow/tests/model/test_mappers.py", line 56, in test_SqliteDb
db._createConnection(self.modelGoldSqlite, timeout=1000)
File "/usr/local/apps/scipion/1.1/pyworkflow/mapper/sqlite_db.py", line 52, in _createConnection
self.connection = sqlite.Connection(dbName, timeout, check_same_thread=False)
OperationalError: unable to open database file
Thanks,
David Hoover
HPC @ NIH
|
|
From: Dmitry S. <sem...@gm...> - 2017-06-12 09:02:27
|
Dear colleagues, The question is about B-factor (over/under-sharpening) How to evaluate the result of the postprocessing and find the optimum B-factor? In my case the B-factor was estimated automatically and equals ~ -112 I experimented with manual B-factor values ( -62; and -172) )and notices that the process_guinier looks differently Auto - case (B-factor= -112) [image: Встроенное изображение 2] B-factor= - 62 [image: Встроенное изображение 3] B-factor= - 172 [image: Встроенное изображение 4] So what seems to change more is AmplitudesSharpened - the red curve. Should this curve be as flat as possible? If there are the other parameters I have to look at? Thank you! Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2017-06-11 21:16:57
|
Hi Dmitry Juha is right, you have a protocol (named 'scipion - extract coordinates') where you can input any set of particles (resulting from grouping after 2D or 3D classification, or any subset of interest) and you can use these coordinates to extract particles in the usual way from a different set of micrographs. Bests, Jose Miguel On Sun, Jun 11, 2017 at 5:48 PM, Juha Huiskonen <ju...@st...> wrote: > Hi Dmitry, > > Yes - there's something called like 'scipion - create coordinates' (others > can correct if I remember inaccurately). Input is a set of particles (e.g. > particles belonging to one class) and output is set of coordinates that can > be used for extraction the usual way. > > Best wishes, > Juha > > On 11 Jun 2017, at 11:36, Dmitry Semchonok <sem...@gm...> wrote: > > Dear colleagues, > > My question is about extraction. > > > I want to extract the original micrographs based on the best particle 3D > class. > > Is that possible? > > Sincerely, > Dmitry > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Juha H. <ju...@st...> - 2017-06-11 15:48:25
|
Hi Dmitry, Yes - there's something called like 'scipion - create coordinates' (others can correct if I remember inaccurately). Input is a set of particles (e.g. particles belonging to one class) and output is set of coordinates that can be used for extraction the usual way. Best wishes, Juha > On 11 Jun 2017, at 11:36, Dmitry Semchonok <sem...@gm...> wrote: > > Dear colleagues, > > My question is about extraction. > > > I want to extract the original micrographs based on the best particle 3D class. > > Is that possible? > > Sincerely, > Dmitry > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Dmitry S. <sem...@gm...> - 2017-06-11 09:37:00
|
Dear colleagues, My question is about extraction. I want to extract the original micrographs based on the best particle 3D class. Is that possible? Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2017-06-05 07:17:01
|
Dear Dieter, Take a look at the help of xmipp_transform_filter, I think the raised_cosine should not be there. The command line should be like: scipion xmipp_transform_filter -i my.vol -o my_filtered.vol --fourier low_pass 30 0.05 --sampling 0.97 Regarding the pixel size, Xmipp does not use or store information in the header of the images/volumes, so that's the reason why still your output volume has pixel size of 1 instead of 0.97 Bests, Jose Miguel On Sun, Jun 4, 2017 at 8:43 AM, Dieter Blaas <die...@me...> wrote: > Dear Pablo and all, > > thanks a lot, I got it! Now I am having the next problem: Trying to > prepare a mask by using a pdb file I first looked for an example with: > > "scipion xmipp_volume_from_pdb" > > and got the following: > > "EXAMPLES > Sample at 1.6A and limit the frequency to 10A > xmipp_volume_from_pdb -i 1o7d.pdb --sampling 1.6 > xmipp_transform_filter -i 1o7d.vol -o 1o7dFiltered.vol --fourier > low_pass 10 raised_cosine 0.05 --sampling 1.6" > > based on this I tried: > > xmipp_volume_from_pdb -i my.pdb --sampling 0.97 > > and got: my.vol > > Next I did: > > scipion xmipp_transform_filter -i my.vol -o my_filtered.vol --fourier > low_pass 30 raised_cosine 0.05 --sampling 0.97 > > and got: > > ** Running command: xmipp_transform_filter "-i" "my.vol" "-o" > "my_filtered.vol" "--fourier" "low_pass" "30" "raised_cosine" "0.05" > "--sampling" "0.97" > XMIPP_ERROR 1: Errors on command line parameters > Too many arguments for parameter --fourier > > File: software/em/xmipp/libraries/data/argsparser.cpp line: 1036 > > *Furthermore:* the generated volume has a sampling of 1 instead of 0.97 > as specified in both commands above. > > Thanks for hints! > > Dieter > > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > Am 22.05.2017 um 08:13 schrieb Pablo Conesa: > > Dear Dieter, you are almost there: > > > after a: > > 1.- git clone https://github.com/I2PC/scipion.git > > 2.- cd scipion > > 3.- git checkout release-1.1 > > you should have release-1.1 code checked out. > > Then continue from here: step2-dependencies > <https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies> > . > > > If you had previous version installed you will need to adjust > configuration files, there are several way to do this, I'll explain the > easiest, this is: > > 1.- Back up your *user config file*. From the console type: *mv > ~/.config/scipion/scipion.conf ~/.config/scipion/scipion.conf.v1.0.backup* > > 2.- Run *scipion config* (this will regenerate you user config file > compatible with release 1.1) > > 3.- run *scipion config --update* (this will update your existing > scipion_home config file with missing new variables) > > 4.- Review EM software folders name, at *<SCIPION_HOME>/software/em/*, > this is the main change from release 1.0 to 1.1. Here you have 2 options: > > A) Simplest way would be to remove all folders there *except xmipp*. > And install EM software needed again using scipion install > <package-version>. Most of them are just a tar.gz extraction. It should be > quick. And some versions have been updated like motioncor2. > > B) RenameEM packages folders (or create links) to match new naming > convention (package-version). As an example, in release 1.0 the folder > for frealign was named "frealign". Now, in release 1.1 it should have the > version also in the name--> frealign-9.07 > > 5.- Compile Xmipp with new code: *scipion install -j 5* > > That should be all to install and migrate configuration from Scipion 1.0 > to Scipion 1.1. > > Let us know how it goes and if you need any further assistance. > > All the best, Pablo. > > Scipion Team. > > On 19/05/17 17:24, Dieter Blaas wrote: > > Hi Juha, Miguel & all, > > please forgive me my ignorance but what is the command for installing > scipion *release-1.1?* Can it be installed via git clone or do I have to > use the tar.gz file? I cannot find the correct name in github! > > Dieter > > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > Am 19.05.2017 um 08:40 schrieb Dieter Blaas: > > Dear all, > > thank you very much for these explanations, I shall do as suggested! > > Best wishes, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > Am 19.05.2017 um 08:11 schrieb Juha Huiskonen: > > Dear Dieter, > > I just checked and Jose Miguel is right, when run localrec from Scipion, > localrec needs to have Relion 1.4 present. So when you install Scipion, > please install both. However, 1.4 is used only internally for some > functions - you can still classify, refine and reconstruct the sub-paricles > in Relion 2.0. > > Please double check that you have this line in your > .config/scipion/scipion.conf file: > LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4 > > Best wishes, > Juha > > > On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > >> Dear Dieter, >> >> As Juha suggested, it would be better to use branch release-1.1, which is >> going to be the next official release. >> >> Juha, correct me if I'm wrong, but I think that localrec would need >> Relion 1.4, and currently does not work with 2.0. In Scipion, both versions >> can live together. Indeed, you don't need to modify your environment, >> Scipion will do it for you when launching Relion jobs (the same for other >> packages). It is also possible to reuse package installations (if the >> version is the one used in Scipion). You just need to create a symbolic >> link in the scipion/software/em folder with the proper name >> (package-version). >> >> Cheers, >> Jose Miguel >> >> >> On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen <ju...@st...> >> wrote: >> >>> Dear Dieter >>> >>> Please update your Scipion to 1.1 beta (balbino) from github branch >>> release-1.1-fixes. Localrec is part of that version and will be in the >>> official release 1.1 when that comes out. It is also compatible with Relion >>> 2.0. >>> >>> Best wishes, >>> Juha >>> >>> On 19 May 2017, at 08:14, Dieter Blaas <die...@me...> >>> wrote: >>> >>> Dear colleagues, >>> >>> I tried to install localrec in scipion (Scipion v1.0.1 >>> (2016-06-30) Augusto) following this instruction: >>> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install but >>> 'scipion >>> --help' does not show this software and 'scipion install localrec' does >>> not find it. >>> >>> 1) how do I install localrec? >>> >>> 2) once installed will it run also by using the latest relion version >>> (i.e. relion-2.0.x, which I have as a separate and independent install) >>> or do I have to use the old relion (v-1.4) and if so, can both version >>> live side by side (for example relion-1.4 within scipion and >>> relion-2.0.5 outside scipion? >>> >>> Thanks a lot for hints, >>> >>> Dieter >>> >>> >>> >>> ------------------------------------------------------------------------ >>> Dieter Blaas, >>> Max F. Perutz Laboratories >>> Medical University of Vienna, >>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>> Dr. Bohr Gasse 9/3, >>> A-1030 Vienna, Austria, >>> Tel: 0043 1 4277 61630, >>> Fax: 0043 1 4277 9616, >>> e-mail: die...@me... >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dieter B. <die...@me...> - 2017-06-04 06:43:52
|
Dear Pablo and all,
thanks a lot, I got it! Now I am having the next problem: Trying to
prepare a mask by using a pdb file I first looked for an example with:
"scipion xmipp_volume_from_pdb"
and got the following:
"EXAMPLES
Sample at 1.6A and limit the frequency to 10A
xmipp_volume_from_pdb -i 1o7d.pdb --sampling 1.6
xmipp_transform_filter -i 1o7d.vol -o 1o7dFiltered.vol
--fourier low_pass 10 raised_cosine 0.05 --sampling 1.6"
based on this I tried:
xmipp_volume_from_pdb -i my.pdb --sampling 0.97
and got: my.vol
Next I did:
scipion xmipp_transform_filter -i my.vol -o my_filtered.vol --fourier
low_pass 30 raised_cosine 0.05 --sampling 0.97
and got:
** Running command: xmipp_transform_filter "-i" "my.vol" "-o"
"my_filtered.vol" "--fourier" "low_pass" "30" "raised_cosine" "0.05"
"--sampling" "0.97"
XMIPP_ERROR 1: Errors on command line parameters
Too many arguments for parameter --fourier
File: software/em/xmipp/libraries/data/argsparser.cpp line: 1036
*Furthermore:* the generated volume has a sampling of 1 instead of 0.97
as specified in both commands above.
Thanks for hints!
Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: die...@me...
------------------------------------------------------------------------
Am 22.05.2017 um 08:13 schrieb Pablo Conesa:
>
> Dear Dieter, you are almost there:
>
>
> after a:
>
> 1.- git clone https://github.com/I2PC/scipion.git
>
> 2.- cd scipion
>
> 3.- git checkout release-1.1
>
> you should have release-1.1 code checked out.
>
> Then continue from here: step2-dependencies
> <https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies>.
>
>
> If you had previous version installed you will need to adjust
> configuration files, there are several way to do this, I'll explain
> the easiest, this is:
>
> 1.- Back up your *user config file*. From the console type: /mv
> ~/.config/scipion/scipion.conf ~/.config/scipion/scipion.conf.v1.0.backup/
>
> 2.- Run /scipion config/ (this will regenerate you user config file
> compatible with release 1.1)
>
> 3.- run /scipion config --update/ (this will update your existing
> scipion_home config file with missing new variables)
>
> 4.- Review EM software folders name, at *<SCIPION_HOME>/software/em/*,
> this is the main change from release 1.0 to 1.1. Here you have 2 options:
>
> A) Simplest way would be to remove all folders there *except
> xmipp*. And install EM software needed again using scipion install
> <package-version>. Most of them are just a tar.gz extraction. It
> should be quick. And some versions have been updated like motioncor2.
>
> B) RenameEM packages folders (or create links) to match new naming
> convention (package-version). As an example, in release 1.0 the folder
> for frealign was named "frealign". Now, in release 1.1 it should have
> the version also in the name--> frealign-9.07
>
> 5.-Compile Xmipp with new code: /scipion install -j 5/
>
> That should be all to install and migrate configuration from Scipion
> 1.0 to Scipion 1.1.
>
>
> Let us know how it goes and if you need any further assistance.
>
> All the best, Pablo.
>
> Scipion Team.
>
> On 19/05/17 17:24, Dieter Blaas wrote:
>>
>> Hi Juha, Miguel & all,
>>
>> please forgive me my ignorance but what is the command for
>> installing scipion *release-1.1?* Can it be installed via git clone
>> or do I have to use the tar.gz file? I cannot find the correct name
>> in github!
>>
>> Dieter*
>> *
>>
>> *
>> *
>>
>> ------------------------------------------------------------------------
>> Dieter Blaas,
>> Max F. Perutz Laboratories
>> Medical University of Vienna,
>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>> Dr. Bohr Gasse 9/3,
>> A-1030 Vienna, Austria,
>> Tel: 0043 1 4277 61630,
>> Fax: 0043 1 4277 9616,
>> e-mail:die...@me...
>> ------------------------------------------------------------------------
>> Am 19.05.2017 um 08:40 schrieb Dieter Blaas:
>>>
>>> Dear all,
>>>
>>> thank you very much for these explanations, I shall do as suggested!
>>>
>>> Best wishes, Dieter
>>>
>>> ------------------------------------------------------------------------
>>> Dieter Blaas,
>>> Max F. Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Fax: 0043 1 4277 9616,
>>> e-mail:die...@me...
>>> ------------------------------------------------------------------------
>>> Am 19.05.2017 um 08:11 schrieb Juha Huiskonen:
>>>> Dear Dieter,
>>>>
>>>> I just checked and Jose Miguel is right, when run localrec from
>>>> Scipion, localrec needs to have Relion 1.4 present. So when you
>>>> install Scipion, please install both. However, 1.4 is used only
>>>> internally for some functions - you can still classify, refine and
>>>> reconstruct the sub-paricles in Relion 2.0.
>>>>
>>>> Please double check that you have this line in your
>>>> .config/scipion/scipion.conf file:
>>>> LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4
>>>>
>>>> Best wishes,
>>>> Juha
>>>>
>>>>
>>>> On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin
>>>> <del...@gm... <mailto:del...@gm...>> wrote:
>>>>
>>>> Dear Dieter,
>>>>
>>>> As Juha suggested, it would be better to use branch
>>>> release-1.1, which is going to be the next official release.
>>>>
>>>> Juha, correct me if I'm wrong, but I think that localrec would
>>>> need Relion 1.4, and currently does not work with 2.0. In
>>>> Scipion, both versions can live together. Indeed, you don't
>>>> need to modify your environment, Scipion will do it for you
>>>> when launching Relion jobs (the same for other packages). It is
>>>> also possible to reuse package installations (if the version is
>>>> the one used in Scipion). You just need to create a symbolic
>>>> link in the scipion/software/em folder with the proper name
>>>> (package-version).
>>>>
>>>> Cheers,
>>>> Jose Miguel
>>>>
>>>>
>>>> On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen
>>>> <ju...@st... <mailto:ju...@st...>> wrote:
>>>>
>>>> Dear Dieter
>>>>
>>>> Please update your Scipion to 1.1 beta (balbino) from
>>>> github branch release-1.1-fixes. Localrec is part of that
>>>> version and will be in the official release 1.1 when that
>>>> comes out. It is also compatible with Relion 2.0.
>>>>
>>>> Best wishes,
>>>> Juha
>>>>
>>>> On 19 May 2017, at 08:14, Dieter Blaas
>>>> <die...@me...
>>>> <mailto:die...@me...>> wrote:
>>>>
>>>>> Dear colleagues,
>>>>>
>>>>> I tried to install localrec in scipion (Scipion v1.0.1
>>>>> (2016-06-30) Augusto) following this instruction:
>>>>> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install
>>>>> <https://github.com/OPIC-Oxford/localrec/wiki/How-to-install>
>>>>> but 'scipion
>>>>> --help' does not show this software and 'scipion install
>>>>> localrec' does
>>>>> not find it.
>>>>>
>>>>> 1) how do I install localrec?
>>>>>
>>>>> 2) once installed will it run also by using the latest
>>>>> relion version
>>>>> (i.e. relion-2.0.x, which I have as a separate and
>>>>> independent install)
>>>>> or do I have to use the old relion (v-1.4) and if so, can
>>>>> both version
>>>>> live side by side (for example relion-1.4 within scipion and
>>>>> relion-2.0.5 outside scipion?
>>>>>
>>>>> Thanks a lot for hints,
>>>>>
>>>>> Dieter
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>> Dieter Blaas,
>>>>> Max F. Perutz Laboratories
>>>>> Medical University of Vienna,
>>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>>> Dr. Bohr Gasse 9/3,
>>>>> A-1030 Vienna, Austria,
>>>>> Tel: 0043 1 4277 61630,
>>>>> Fax: 0043 1 4277 9616,
>>>>> e-mail: die...@me...
>>>>> <mailto:die...@me...>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's
>>>>> most
>>>>> engaging tech sites, Slashdot.org <http://Slashdot.org>!
>>>>> http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> scipion-users mailing list
>>>>> sci...@li...
>>>>> <mailto:sci...@li...>
>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> <mailto:sci...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org!http://sdm.link/slashdot
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org!http://sdm.link/slashdot
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: JOSE L. V. P. <jl...@cn...> - 2017-05-30 13:02:28
|
Dear Dimitry, As MonoRes input you can use both, in my opinion use the best result. Usually is common to use the postprocessing, however, in this case if you consider that the autorefinement offers better quality then use the autorefinement About the usage of MonoRes: > *Is the original premasked?* *Y/N* Sometimes the reconstructed volume is inside a sphere (circular mask). This parameter ought to be set as yes if the volume is inside a sphere. (By default - No), but this depends on your processing. > *Filter input volume with local resolution? Y/N* If you enable this option, you will get the local resolution map and moreover your map will be locally low pass filtered at the local resolution value. Regards José Luis Vilas Quoting Dmitry Semchonok <sem...@gm...>: > Dear colleagues, > > Could you please tell me which file shall I use as an input for *xmipp3-local > MonoRes* - > > relion-3D autoref or > relion postprocessing? > > I tried them both and the results are a little different - (better with > relion 3D autoref) > > > > And coming from that question - > > The usage of > > *Is the original premasked?* *Y/N* > > > *Filter input volume with local resolution? Y/N* > > > In what case have I enable/disable those functions? (I kept them disabled) > > > Sincerely, > Dmitry |
|
From: Dmitry S. <sem...@gm...> - 2017-05-30 10:05:18
|
Dear colleagues, Could you please tell me which file shall I use as an input for *xmipp3-local MonoRes* - relion-3D autoref or relion postprocessing? I tried them both and the results are a little different - (better with relion 3D autoref) And coming from that question - The usage of *Is the original premasked?* *Y/N* *Filter input volume with local resolution? Y/N* In what case have I enable/disable those functions? (I kept them disabled) Sincerely, Dmitry |
|
From: Pablo C. <su...@bc...> - 2017-05-29 17:34:02
|
Hi Dmitry,
We have also done some changes recently in monoRes, and the developer thinks latest changes could also fix the issue.
So to do that just need to do the standard procedure:
From the scipion home folder:
git pull
./scipion install -j 5
Since you are in a cluster, better ask the admins to to this.
Thanks once more for the feedback.
All the best, Pablo.
Scipion team
Activo Lun, 29 Mayo at 4:30 PM
, Biocomputing unit - National Center for Biotechnology <sc...@cn...> Escrito:
On 29/05/17 16:17, Dmitry Semchonok
wrote:
Dear Pablo,
Yes indeed it is a
cluster.
I already
envisaged this option
and contacted the admin at the same time :). But currently
no reply...
Thank you.
Sincerely,
Dmitry
On
May 29, 2017 16:05:46 Pablo Conesa
<pc...@cn...> wrote:
Hi Dmitry, is that your machine or a cluster.
If it's a Cluster, then you should talk to the cluster
admins, they should know what is this about,
If it's your machine, you should have cmake installed in
your machine.
On 29/05/17 10:15, Dmitry
Semchonok wrote:
Dear Pablo,
Thank you very much for the answer.
When I tried the command: scipion install -j
5
I ended up with the error
Error: Cannot run
'cmake'. Please install it in your system first.
Am I doing something
wrong?
Sincerely,
Dmitry
2017-05-28 20:13 GMT+02:00
Pablo Conesa - CNB <p.c...@gm...>:
Hi
Dmitry, every time you update the code (git
pull....or git checkout) you are bringing new code
to your computer.
This, depending on what has changed might require
compiling Xmipp again, which looks like it's what is
happening.
Try to run from the command line:
scipion install -j 5
If I remember right you run scipion without "./"
Try this and run localMonoRes again.
> On 27 May 2017, at 13:20, Dmitry Semchonok
<sem...@gm...>
wrote:
>
> Dear colleague,
>
> Using xmipp3-localMonoRes I get the error.
>
> The parameters used - (input from
relion-postprocessing; the same for the binary
mask)
>
> <изображение.png>
>
>
> The error
>
> XMIPP_ERROR 1: Errors on command line
parameters
> 00019: Unrecognized parameter: --mask_out
> 00020: Unrecognized parameter:
--md_outputdata
> 00021:
> 00022: File:
software/em/xmipp/libraries/data/argsparser.cpp
line: 1036
>
> <изображение.png>
>
> <изображение.png>
>
>
>
>
> Any ideas what can be done?
>
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
>
>
>
------------------------------------------------------------------------------
> Check out the vibrant tech community on one of
the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Pablo C. - C. <p.c...@gm...> - 2017-05-28 18:13:50
|
Hi Dmitry, every time you update the code (git pull....or git checkout) you are bringing new code to your computer. This, depending on what has changed might require compiling Xmipp again, which looks like it's what is happening. Try to run from the command line: scipion install -j 5 If I remember right you run scipion without "./" Try this and run localMonoRes again. > On 27 May 2017, at 13:20, Dmitry Semchonok <sem...@gm...> wrote: > > Dear colleague, > > Using xmipp3-localMonoRes I get the error. > > The parameters used - (input from relion-postprocessing; the same for the binary mask) > > <изображение.png> > > > The error > > XMIPP_ERROR 1: Errors on command line parameters > 00019: Unrecognized parameter: --mask_out > 00020: Unrecognized parameter: --md_outputdata > 00021: > 00022: File: software/em/xmipp/libraries/data/argsparser.cpp line: 1036 > > <изображение.png> > > <изображение.png> > > > > > Any ideas what can be done? > > > Thank you! > > Sincerely, > Dmitry > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Dmitry S. <sem...@gm...> - 2017-05-27 11:20:19
|
Dear colleague, Using xmipp3-localMonoRes I get the error. The parameters used - (input from relion-postprocessing; the same for the binary mask) [image: Встроенное изображение 3] The error XMIPP_ERROR 1: Errors on command line parameters 00019: Unrecognized parameter: --mask_out 00020: Unrecognized parameter: --md_outputdata 00021: 00022: File: software/em/xmipp/libraries/data/argsparser.cpp line: 1036 [image: Встроенное изображение 4] [image: Встроенное изображение 6] Any ideas what can be done? Thank you! Sincerely, Dmitry |
|
From: Laura d. C. <su...@bc...> - 2017-05-26 10:18:47
|
Hi Valerie,
what do you mean with 'desktop computer that does not have MPI facility'? You mean it does not have openmpi package installed?
It is not a problem to install it if you have administrator privileges but if you dont want to you can use relion and other programs inside Scipion without MPIs, just using threads. Some tests are predefine to use MPIs (such as Relion classification 2D) but if you want to run them you could change it manually on the python script, I can tell you where.
let me know
Laura
Activo Mie, 24 Mayo at 12:06 PM
, Valerie.biou <val...@ib...> Escrito:
Hi Laura, it's nice that you asked about this. the answer is that I haven't solved the problem but I have an idea: I talked yesterday with a person from our institute who found out that the programs that don't run all have issues with MPI. I am using a desktop computer that does not have MPI facility so it seems that MPI is failing because of this. we saw that relion executables come in two versions: with and without mpi relion_autopick relion_project relion_autopick_mpi relion_qsub.csh relion_display relion_reconstruct relion_find_tiltpairs relion_refine relion_helix_toolbox relion_refine_mpi relion_image_handler relion_run_ctffind relion_maingui relion_run_ctffind_mpi relion_manualpick relion_run_motioncorr relion_mask_create relion_run_motioncorr_mpi relion_particle_polish relion_stack_create relion_particle_polish_mpi relion_star_combine relion_particle_reposition relion_star_compare relion_particle_sort relion_star_datablock_ctfdat relion_particle_sort_mpi relion_star_datablock_singlefiles relion_particle_symmetry_expand relion_star_datablock_stack relion_pipeliner relion_star_loopheader relion_postprocess relion_star_plottable relion_postprocess_mpi relion_star_printtable relion_preprocess relion_tiltpair_plot so my question is : is there a way to configure scipion so it calls the non-mpi executables? Cheers, Valérie Biou Laboratoire de Biologie Physico-Chimique des Protéines Membranaires UMR 7099 CNRS/Univ. Paris Diderot P7 Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France Tel : +33 (0)1 5841 5099 Fax : +33 (0)1 5841 5024 ----- Mail original ----- De: "Laura del Caño" <su...@bc...> À: "Valerie Biou" <val...@ib...> Cc: sci...@li... Envoyé: Mercredi 24 Mai 2017 11:38:41 Objet: Re: [scipion-users] test for relion 2D classification failed: MPI error Hi Valerie.biou, Did you solve this problem with relion classification test? cheers Laura Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/119 Activo Vie, 28 Abril at 11:02 AM , Valerie.biou <val...@ib...> Escrito: Hello the test for 2D classification using CL2D worked and I tried to run the test for 2D classification using Relion which failed with an MPI error (see attached log file). Do you have any suggestion? thanks, best regards Valérie Biou Laboratoire de Biologie Physico-Chimique des Protéines Membranaires UMR 7099 CNRS/Univ. Paris Diderot P7 Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France
|
|
From: Yaiza R. <su...@bc...> - 2017-05-24 10:14:58
|
Hi Dmitry,
It looks like the protocol is having trouble finding your movies, have they moved or have you moved your project recently? Can you try importing them again and executing this right afterwards?
Best,
Yaiza Rancel
Scipion Team
Activo Dom, 14 Mayo at 12:01 PM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues,
The protocol xmipp3 - movie extract ends up with the following error STARTED: processMovieStep, step 1 00012: 2017-05-14 10:42:24.500805 00013: Processing movie: Runs/028262_XmippProtExtractMovieParticles/tmp/movie_000001/FoilHole_26594250_Data_25564800_25564801_20160826_2007-21923.mrc 00014: Traceback (most recent call last): 00015: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py", line 182, in run 00016: self._run() 00017: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py", line 228, in _run 00018: resultFiles = self._runFunc() 00019: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py", line 224, in _runFunc 00020: return self._func(*self._args) 00021: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_movies.py", line 267, in processMovieStep 00022: self._processMovie(movie) 00023: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/packages/xmipp3/protocol_extract_particles_movies.py", line 191, in _processMovie 00024: x, y, n = movie.getDim() 00025: TypeError: 'NoneType' object is not iterable 00026: Protocol failed: 'NoneType' object is not iterable 00027: FAILED: processMovieStep, step 1 00028: 2017-05-14 10:42:25.035791 00029: ------------------- PROTOCOL FAILED (DONE 1/5141) ```````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````` 00001: 2017-05-14 10:42:18,291 INFO: RUNNING PROTOCOL ----------------- 00002: 2017-05-14 10:42:18,292 INFO: PID: 58347 00003: 2017-05-14 10:42:18,292 INFO: Scipion: v1.1-beta (2017-04-21) Balbino 00004: 2017-05-14 10:42:18,292 INFO: currentDir: /scratch/p260888/ScipionUserData/projects/tetra_parts_ 00005: 2017-05-14 10:42:18,293 INFO: workingDir: Runs/028262_XmippProtExtractMovieParticles 00006: 2017-05-14 10:42:18,293 INFO: runMode: Restart 00007: 2017-05-14 10:42:18,293 INFO: MPI: 1 00008: 2017-05-14 10:42:18,293 INFO: threads: 1 00009: 2017-05-14 10:42:22,697 INFO: Starting at step: 1 00010: 2017-05-14 10:42:24,443 INFO: Running steps 00011: 2017-05-14 10:42:24,500 INFO: STARTED: processMovieStep, step 1 00012: 2017-05-14 10:42:24,501 INFO: 2017-05-14 10:42:24.500805 00013: 2017-05-14 10:42:25,034 INFO: Processing movie: Runs/028262_XmippProtExtractMovieParticles/tmp/movie_000001/FoilHole_26594250_Data_25564800_25564801_20160826_2007-21923.mrc 00014: 2017-05-14 10:42:25,037 ERROR: Protocol failed: 'NoneType' object is not iterable 00015: 2017-05-14 10:42:25,126 INFO: FAILED: processMovieStep, step 1 00016: 2017-05-14 10:42:25,126 INFO: 2017-05-14 10:42:25.035791 00017: 2017-05-14 10:42:25,308 INFO: ------------------- PROTOCOL FAILED (DONE 1/5141) 00018: 2017-05-14 10:42:29,073 INFO: ------------------- PROTOCOL FAILED (DONE 1/5141)
Any ideas how to fix that?
Thank you
Sincerely,
Dmitry Scipion v1.1-beta (2017-04-21) Balbino
|
|
From: Laura d. C. <su...@bc...> - 2017-05-24 09:57:09
|
Hi Valerie.biou, Did you solve this problem with relion classification test? cheers Laura Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/119 Activo Vie, 28 Abril at 11:02 AM , Valerie.biou <val...@ib...> Escrito: Hello the test for 2D classification using CL2D worked and I tried to run the test for 2D classification using Relion which failed with an MPI error (see attached log file). Do you have any suggestion? thanks, best regards Valérie Biou Laboratoire de Biologie Physico-Chimique des Protéines Membranaires UMR 7099 CNRS/Univ. Paris Diderot P7 Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France |
|
From: Pablo C. <pc...@cn...> - 2017-05-22 06:14:13
|
Dear Dieter, you are almost there: after a: 1.- git clone https://github.com/I2PC/scipion.git 2.- cd scipion 3.- git checkout release-1.1 you should have release-1.1 code checked out. Then continue from here: step2-dependencies <https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies>. If you had previous version installed you will need to adjust configuration files, there are several way to do this, I'll explain the easiest, this is: 1.- Back up your *user config file*. From the console type: /mv ~/.config/scipion/scipion.conf ~/.config/scipion/scipion.conf.v1.0.backup/ 2.- Run /scipion config/ (this will regenerate you user config file compatible with release 1.1) 3.- run /scipion config --update/ (this will update your existing scipion_home config file with missing new variables) 4.- Review EM software folders name, at *<SCIPION_HOME>/software/em/*, this is the main change from release 1.0 to 1.1. Here you have 2 options: A) Simplest way would be to remove all folders there *except xmipp*. And install EM software needed again using scipion install <package-version>. Most of them are just a tar.gz extraction. It should be quick. And some versions have been updated like motioncor2. B) RenameEM packages folders (or create links) to match new naming convention (package-version). As an example, in release 1.0 the folder for frealign was named "frealign". Now, in release 1.1 it should have the version also in the name--> frealign-9.07 5.-Compile Xmipp with new code: /scipion install -j 5/ That should be all to install and migrate configuration from Scipion 1.0 to Scipion 1.1. Let us know how it goes and if you need any further assistance. All the best, Pablo. Scipion Team. On 19/05/17 17:24, Dieter Blaas wrote: > > Hi Juha, Miguel & all, > > please forgive me my ignorance but what is the command for > installing scipion *release-1.1?* Can it be installed via git clone or > do I have to use the tar.gz file? I cannot find the correct name in > github! > > Dieter* > * > > * > * > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail:die...@me... > ------------------------------------------------------------------------ > Am 19.05.2017 um 08:40 schrieb Dieter Blaas: >> >> Dear all, >> >> thank you very much for these explanations, I shall do as suggested! >> >> Best wishes, Dieter >> >> ------------------------------------------------------------------------ >> Dieter Blaas, >> Max F. Perutz Laboratories >> Medical University of Vienna, >> Inst. Med. Biochem., Vienna Biocenter (VBC), >> Dr. Bohr Gasse 9/3, >> A-1030 Vienna, Austria, >> Tel: 0043 1 4277 61630, >> Fax: 0043 1 4277 9616, >> e-mail:die...@me... >> ------------------------------------------------------------------------ >> Am 19.05.2017 um 08:11 schrieb Juha Huiskonen: >>> Dear Dieter, >>> >>> I just checked and Jose Miguel is right, when run localrec from >>> Scipion, localrec needs to have Relion 1.4 present. So when you >>> install Scipion, please install both. However, 1.4 is used only >>> internally for some functions - you can still classify, refine and >>> reconstruct the sub-paricles in Relion 2.0. >>> >>> Please double check that you have this line in your >>> .config/scipion/scipion.conf file: >>> LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4 >>> >>> Best wishes, >>> Juha >>> >>> >>> On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin >>> <del...@gm... <mailto:del...@gm...>> wrote: >>> >>> Dear Dieter, >>> >>> As Juha suggested, it would be better to use branch release-1.1, >>> which is going to be the next official release. >>> >>> Juha, correct me if I'm wrong, but I think that localrec would >>> need Relion 1.4, and currently does not work with 2.0. In >>> Scipion, both versions can live together. Indeed, you don't need >>> to modify your environment, Scipion will do it for you when >>> launching Relion jobs (the same for other packages). It is also >>> possible to reuse package installations (if the version is the >>> one used in Scipion). You just need to create a symbolic link in >>> the scipion/software/em folder with the proper name >>> (package-version). >>> >>> Cheers, >>> Jose Miguel >>> >>> >>> On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen >>> <ju...@st... <mailto:ju...@st...>> wrote: >>> >>> Dear Dieter >>> >>> Please update your Scipion to 1.1 beta (balbino) from github >>> branch release-1.1-fixes. Localrec is part of that version >>> and will be in the official release 1.1 when that comes out. >>> It is also compatible with Relion 2.0. >>> >>> Best wishes, >>> Juha >>> >>> On 19 May 2017, at 08:14, Dieter Blaas >>> <die...@me... >>> <mailto:die...@me...>> wrote: >>> >>>> Dear colleagues, >>>> >>>> I tried to install localrec in scipion (Scipion v1.0.1 >>>> (2016-06-30) Augusto) following this instruction: >>>> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install >>>> <https://github.com/OPIC-Oxford/localrec/wiki/How-to-install> >>>> but 'scipion >>>> --help' does not show this software and 'scipion install >>>> localrec' does >>>> not find it. >>>> >>>> 1) how do I install localrec? >>>> >>>> 2) once installed will it run also by using the latest >>>> relion version >>>> (i.e. relion-2.0.x, which I have as a separate and >>>> independent install) >>>> or do I have to use the old relion (v-1.4) and if so, can >>>> both version >>>> live side by side (for example relion-1.4 within scipion and >>>> relion-2.0.5 outside scipion? >>>> >>>> Thanks a lot for hints, >>>> >>>> Dieter >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> Dieter Blaas, >>>> Max F. Perutz Laboratories >>>> Medical University of Vienna, >>>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>>> Dr. Bohr Gasse 9/3, >>>> A-1030 Vienna, Austria, >>>> Tel: 0043 1 4277 61630, >>>> Fax: 0043 1 4277 9616, >>>> e-mail: die...@me... >>>> <mailto:die...@me...> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org <http://Slashdot.org>! >>>> http://sdm.link/slashdot >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> <mailto:sci...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> >>> >>> >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Veli-Pekka K. <vp...@gu...> - 2017-05-20 16:24:51
|
Hi, I got it also working. Another change I needed to do was to change following line: software/em/xmipp/scipion_sconscript: kwargs['libs'] += ['mpi', 'mpi_cxx', 'XmippParallel'] to software/em/xmipp/scipion_sconscript: kwargs['libs'] += ['mpi', 'mpicxx', 'XmippParallel'] as it seems that cluster recommended intel mpi doesn't have underscore in library name. Thanks for the help, -vpk On 17.5.2017 12:47, Juha Huiskonen wrote: > Hi Jose Miguel > > Thanks, this worked for me. > > Best wishes, > Juha > > > On Wed, May 17, 2017 at 10:55 AM, Jose Miguel de la Rosa Trevin > <del...@gm... <mailto:del...@gm...>> wrote: > > Hi Veli-Pekka, > > I have found a line that can be causing that LD_LIBRARY_PATH is not > propagated. > > In line 227 of scipion/SConstruct file, a new Environment is created > and it seems that propagating the whole system environment has > broken other compilations. > So, in the next line the PATH is explicitly propagated. > > Could you try to add the following code in line 229: > > env2['ENV']['LD_LIBRARY_PATH'] = env['ENV']['LD_LIBRARY_PATH'] > > > And check if this solves the specific problem you are having. If it > does, then we will need to consider this change > and if it does not affect other systems. > > > Cheers, > Jose Miguel > > > > On Tue, May 16, 2017 at 10:39 PM, Jose Miguel de la Rosa Trevin > <del...@gm... <mailto:del...@gm...>> wrote: > > Hum, this seems weird. To the best of my knowledge Scons should > preserve the system LD_LIBRARY_PATH, but it seems that is not > working in this way. I will take a look at it tomorrow and think > in a workaround for you can proceed with the installation. > > Veli-Pekka, I'm afraid that now you need to compile all the > required libraries before getting into the Xmipp part. I would > like to improve this for the future, but we are not there yet. > > Bests, > Jose Miguel > > > On Tue, May 16, 2017 at 10:31 PM, Veli-Pekka Kestilä > <vp...@gu... <mailto:vp...@gu...>> wrote: > > > Hi, > > I checked this and Juha was correct in his theory on missing > LD_LIBRARY_PATH. It seems that CSC has changed their > environment so that > for g++ it's mandatory to have libcloog in LD_LIBRARY_PATH > and scipion > or scons strips it away from it. > > If I manually remove libcloog from the LD_LIBRARY_PATH the > error also > manifested itself in command line. I think the easiest fix > for us would > be that scipion/scons would respect the system > LD_LIBRARY_PATH and would > not change it. > > Is there easy way to skip all the other compilations and > just try > compile xmipp so that I could check if other compilers > provided in the > cluster environment would work? > > Greetings, > -vpk > > On 16.5.2017 16:46, Juha Huiskonen wrote: > > Hi Pablo, > > > > I have these flags: > > > > CCFLAGS = -std=c99 > > CXXFLAGS = > > > > The missing file is on our system in /appl/opt/cloog/0.18.1/lib/ and > > this directory is in my LD_LIBRARY_PATH. > > > > Is it possible that the LD_LIBRARY_PATH is not carried out to scipion > > environment when it tries to compile Xmipp? > > > > Best wishes, > > Juha > > > > On Tue, May 16, 2017 at 2:34 PM, Pablo Conesa <pc...@cn... <mailto:pc...@cn...> > > <mailto:pc...@cn... <mailto:pc...@cn...>>> wrote: > > > > Dear all, we don't think we have committed any recent change here > > that might has cause the issue. > > > > Does anyone know which binary requires the missing library? > > > > And ldd of software/lib/libXmippAlglib.so doesn't seem to depend on it: > > > > linux-vdso.so.1 => (0x00007ffeefd72000) > > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > > (0x00007f026fc53000) > > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f026f94a000) > > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > > (0x00007f026f733000) > > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f026f36a000) > > /lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000) > > > > Am I missing (probably since I'm out of my comfort zone here, this > > is C++) anything? > > > > All the best, Pablo. > > > > > > Could you also send what is the content of the below variables at > > <SCIPIOn_HOME>/config/scipion.conf ? > > > > CCFLAGS, CXXFLAGS > > > > and Does an /echo $CCFLAGS $CXXFLAGS///print something? > > > > > > On 15/05/17 15:35, Juha Huiskonen wrote: > >> Hi Jose Miguel, > >> > >> I am trying to install on the same cluster as Veli-Pekka. I had > >> created the directory in March the 13th, but I am not sure if > >> that's when I last time successfully installed release-1.1 branch. > >> > >> Best wishes, > >> Juha > >> > >> On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin > >> <del...@gm... <mailto:del...@gm...> > <mailto:del...@gm... > <mailto:del...@gm...>>> wrote: > >> > >> Dear Veli-Pekka and Juha, > >> > >> Thanks for the feedback. Juha, do you remember (approximately) > >> when do you successfully installed the branch release-1.1? Is > >> you OS also a CentOS distribution? > >> > >> I have been looking into the logs but none of the recent > >> commits looks like causing such error. > >> > >> Bests, > >> Jose Miguel > >> > >> > >> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen > >> <ju...@st... <mailto:ju...@st...> > <mailto:ju...@st... <mailto:ju...@st...>>> > wrote: > >> > >> Hi All, > >> > >> Just to confirm, I have the same issue as Veli-Pekka > >> reported. I had earlier installed release-1.1 > >> successfully but now after doing "git pull; scipion > >> install" I get an error that it cannot find > >> libcloog-isl.so.4. Any ideas? Perhaps this is something > >> that the the local sysadmins should install? > >> > >> Best wishes, > >> Juha > >> > >> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä > >> <vp...@gu... <mailto:vp...@gu...> <mailto:vp...@gu... > <mailto:vp...@gu...>>> wrote: > >> > >> > >> Hi, > >> > >> I am trying to compile Scipion 1.1 for cluster > >> (taito.csc.fi <http://taito.csc.fi> > <http://taito.csc.fi>) where > >> computing nodes are running CentOS 6.9 > unfortunately > >> compilation fails > >> when compiling Xmipp as the alg-library > it contains > >> needs newer version > >> of cloog library than the system has. > >> > >> I tried to fix the problem by compiling > Cloog library > >> myself, but this > >> didn't work with SCons as it for some > reason makes g++ > >> to ignore shared > >> library infomation. Same compilation on > commanline > >> works without problem > >> > >> scons: done reading SConscript files. > >> scons: Building targets ... > >> g++ -o > software/em/xmipp/external/alglib/src/ap.os -c > >> -DCLOOG_INT_GMP=1 > >> > -I/proj/group/taito/scipion-1.1-fixes/software/include > >> > -L/proj/group/taito/scipion-1.1-fixes/software/lib > >> -L/lib -lcloog-isl > >> -lgmp -O3 -fPIC -Isoftware/include > >> -Isoftware/em/xmipp/external > >> -Isoftware/em/xmipp/libraries > -Isoftware/include > >> software/em/xmipp/external/alglib/src/ap.cpp > >> > /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: > >> error while loading shared libraries: > >> libcloog-isl.so.4: cannot open > >> shared object file: No such file or directory > >> scons: *** > >> > [software/em/xmipp/external/alglib/src/ap.os] Error 1 > >> scons: building terminated because of errors. > >> > >> As as can be seen from the directory > listing file is > >> in given libpath. > >> > >> [user@taito-login4 scipion-1.1-fixes]$ ls -la > >> > /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo* > >> ..../lib/libcloog-isl.a > >> ..../lib/libcloog-isl.la > <http://libcloog-isl.la> <http://libcloog-isl.la> > >> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 > >> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 > >> ..../lib/libcloog-isl.so.4.0.0 > >> > >> I have also tried other ways to give the shared > >> library to the Scons but > >> they have also failed. Any help on the matter is > >> appreciated. > >> > >> Best Regards, > >> Veli-Pekka Kestilä > >> > >> > >> ------------------------------------------------------------------------------ > >> Check out the vibrant tech community on one of the > >> world's most > >> engaging tech sites, Slashdot.org! > >> http://sdm.link/slashdot > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > <mailto:sci...@li...> > >> > <mailto:sci...@li... > <mailto:sci...@li...>> > >> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > >> <https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users>> > >> > >> > >> > >> ------------------------------------------------------------------------------ > >> Check out the vibrant tech community on one of the world's > >> most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > <mailto:sci...@li...> > >> <mailto:sci...@li... > <mailto:sci...@li...>> > >> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > >> <https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users>> > >> > >> > >> > >> > >> > >> ------------------------------------------------------------------------------ > >> Check out the vibrant tech community on one of the world's most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> > >> > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > <mailto:sci...@li...> > >> <mailto:sci...@li... > <mailto:sci...@li...>> > >> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > >> <https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users>> > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > <mailto:sci...@li...> > > <mailto:sci...@li... > <mailto:sci...@li...>> > > > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > <https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users>> > > > > > > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's > most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > <mailto:sci...@li...> > > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > -- Veli-Pekka Kestilä / vp...@gu... / +358503000014 |
|
From: Dieter B. <die...@me...> - 2017-05-19 15:24:49
|
Hi Juha, Miguel & all,
please forgive me my ignorance but what is the command for
installing scipion *release-1.1?* Can it be installed via git clone or
do I have to use the tar.gz file? I cannot find the correct name in github!
Dieter*
*
*
*
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: die...@me...
------------------------------------------------------------------------
Am 19.05.2017 um 08:40 schrieb Dieter Blaas:
>
> Dear all,
>
> thank you very much for these explanations, I shall do as suggested!
>
> Best wishes, Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail:die...@me...
> ------------------------------------------------------------------------
> Am 19.05.2017 um 08:11 schrieb Juha Huiskonen:
>> Dear Dieter,
>>
>> I just checked and Jose Miguel is right, when run localrec from
>> Scipion, localrec needs to have Relion 1.4 present. So when you
>> install Scipion, please install both. However, 1.4 is used only
>> internally for some functions - you can still classify, refine and
>> reconstruct the sub-paricles in Relion 2.0.
>>
>> Please double check that you have this line in your
>> .config/scipion/scipion.conf file:
>> LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4
>>
>> Best wishes,
>> Juha
>>
>>
>> On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin
>> <del...@gm... <mailto:del...@gm...>> wrote:
>>
>> Dear Dieter,
>>
>> As Juha suggested, it would be better to use branch release-1.1,
>> which is going to be the next official release.
>>
>> Juha, correct me if I'm wrong, but I think that localrec would
>> need Relion 1.4, and currently does not work with 2.0. In
>> Scipion, both versions can live together. Indeed, you don't need
>> to modify your environment, Scipion will do it for you when
>> launching Relion jobs (the same for other packages). It is also
>> possible to reuse package installations (if the version is the
>> one used in Scipion). You just need to create a symbolic link in
>> the scipion/software/em folder with the proper name
>> (package-version).
>>
>> Cheers,
>> Jose Miguel
>>
>>
>> On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen
>> <ju...@st... <mailto:ju...@st...>> wrote:
>>
>> Dear Dieter
>>
>> Please update your Scipion to 1.1 beta (balbino) from github
>> branch release-1.1-fixes. Localrec is part of that version
>> and will be in the official release 1.1 when that comes out.
>> It is also compatible with Relion 2.0.
>>
>> Best wishes,
>> Juha
>>
>> On 19 May 2017, at 08:14, Dieter Blaas
>> <die...@me...
>> <mailto:die...@me...>> wrote:
>>
>>> Dear colleagues,
>>>
>>> I tried to install localrec in scipion (Scipion v1.0.1
>>> (2016-06-30) Augusto) following this instruction:
>>> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install
>>> <https://github.com/OPIC-Oxford/localrec/wiki/How-to-install>
>>> but 'scipion
>>> --help' does not show this software and 'scipion install
>>> localrec' does
>>> not find it.
>>>
>>> 1) how do I install localrec?
>>>
>>> 2) once installed will it run also by using the latest
>>> relion version
>>> (i.e. relion-2.0.x, which I have as a separate and
>>> independent install)
>>> or do I have to use the old relion (v-1.4) and if so, can
>>> both version
>>> live side by side (for example relion-1.4 within scipion and
>>> relion-2.0.5 outside scipion?
>>>
>>> Thanks a lot for hints,
>>>
>>> Dieter
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> Dieter Blaas,
>>> Max F. Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Fax: 0043 1 4277 9616,
>>> e-mail: die...@me...
>>> <mailto:die...@me...>
>>> ------------------------------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org <http://Slashdot.org>!
>>> http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> <mailto:sci...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> <mailto:sci...@li...>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>>
>>
>>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Dieter B. <die...@me...> - 2017-05-19 06:40:24
|
Dear all,
thank you very much for these explanations, I shall do as suggested!
Best wishes, Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: die...@me...
------------------------------------------------------------------------
Am 19.05.2017 um 08:11 schrieb Juha Huiskonen:
> Dear Dieter,
>
> I just checked and Jose Miguel is right, when run localrec from
> Scipion, localrec needs to have Relion 1.4 present. So when you
> install Scipion, please install both. However, 1.4 is used only
> internally for some functions - you can still classify, refine and
> reconstruct the sub-paricles in Relion 2.0.
>
> Please double check that you have this line in your
> .config/scipion/scipion.conf file:
> LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4
>
> Best wishes,
> Juha
>
>
> On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin
> <del...@gm... <mailto:del...@gm...>> wrote:
>
> Dear Dieter,
>
> As Juha suggested, it would be better to use branch release-1.1,
> which is going to be the next official release.
>
> Juha, correct me if I'm wrong, but I think that localrec would
> need Relion 1.4, and currently does not work with 2.0. In Scipion,
> both versions can live together. Indeed, you don't need to modify
> your environment, Scipion will do it for you when launching Relion
> jobs (the same for other packages). It is also possible to reuse
> package installations (if the version is the one used in Scipion).
> You just need to create a symbolic link in the scipion/software/em
> folder with the proper name (package-version).
>
> Cheers,
> Jose Miguel
>
>
> On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen
> <ju...@st... <mailto:ju...@st...>> wrote:
>
> Dear Dieter
>
> Please update your Scipion to 1.1 beta (balbino) from github
> branch release-1.1-fixes. Localrec is part of that version and
> will be in the official release 1.1 when that comes out. It is
> also compatible with Relion 2.0.
>
> Best wishes,
> Juha
>
> On 19 May 2017, at 08:14, Dieter Blaas
> <die...@me...
> <mailto:die...@me...>> wrote:
>
>> Dear colleagues,
>>
>> I tried to install localrec in scipion (Scipion v1.0.1
>> (2016-06-30) Augusto) following this instruction:
>> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install
>> <https://github.com/OPIC-Oxford/localrec/wiki/How-to-install>
>> but 'scipion
>> --help' does not show this software and 'scipion install
>> localrec' does
>> not find it.
>>
>> 1) how do I install localrec?
>>
>> 2) once installed will it run also by using the latest relion
>> version
>> (i.e. relion-2.0.x, which I have as a separate and
>> independent install)
>> or do I have to use the old relion (v-1.4) and if so, can
>> both version
>> live side by side (for example relion-1.4 within scipion and
>> relion-2.0.5 outside scipion?
>>
>> Thanks a lot for hints,
>>
>> Dieter
>>
>>
>>
>> ------------------------------------------------------------------------
>> Dieter Blaas,
>> Max F. Perutz Laboratories
>> Medical University of Vienna,
>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>> Dr. Bohr Gasse 9/3,
>> A-1030 Vienna, Austria,
>> Tel: 0043 1 4277 61630,
>> Fax: 0043 1 4277 9616,
>> e-mail: die...@me...
>> <mailto:die...@me...>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://Slashdot.org>!
>> http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> <mailto:sci...@li...>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
>
>
|
|
From: Juha H. <ju...@st...> - 2017-05-19 06:12:29
|
Dear Dieter, I just checked and Jose Miguel is right, when run localrec from Scipion, localrec needs to have Relion 1.4 present. So when you install Scipion, please install both. However, 1.4 is used only internally for some functions - you can still classify, refine and reconstruct the sub-paricles in Relion 2.0. Please double check that you have this line in your .config/scipion/scipion.conf file: LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4 Best wishes, Juha On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Dear Dieter, > > As Juha suggested, it would be better to use branch release-1.1, which is > going to be the next official release. > > Juha, correct me if I'm wrong, but I think that localrec would need Relion > 1.4, and currently does not work with 2.0. In Scipion, both versions can > live together. Indeed, you don't need to modify your environment, Scipion > will do it for you when launching Relion jobs (the same for other > packages). It is also possible to reuse package installations (if the > version is the one used in Scipion). You just need to create a symbolic > link in the scipion/software/em folder with the proper name > (package-version). > > Cheers, > Jose Miguel > > > On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen <ju...@st...> > wrote: > >> Dear Dieter >> >> Please update your Scipion to 1.1 beta (balbino) from github branch >> release-1.1-fixes. Localrec is part of that version and will be in the >> official release 1.1 when that comes out. It is also compatible with Relion >> 2.0. >> >> Best wishes, >> Juha >> >> On 19 May 2017, at 08:14, Dieter Blaas <die...@me...> >> wrote: >> >> Dear colleagues, >> >> I tried to install localrec in scipion (Scipion v1.0.1 >> (2016-06-30) Augusto) following this instruction: >> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install but 'scipion >> --help' does not show this software and 'scipion install localrec' does >> not find it. >> >> 1) how do I install localrec? >> >> 2) once installed will it run also by using the latest relion version >> (i.e. relion-2.0.x, which I have as a separate and independent install) >> or do I have to use the old relion (v-1.4) and if so, can both version >> live side by side (for example relion-1.4 within scipion and >> relion-2.0.5 outside scipion? >> >> Thanks a lot for hints, >> >> Dieter >> >> >> >> ------------------------------------------------------------------------ >> Dieter Blaas, >> Max F. Perutz Laboratories >> Medical University of Vienna, >> Inst. Med. Biochem., Vienna Biocenter (VBC), >> Dr. Bohr Gasse 9/3, >> A-1030 Vienna, Austria, >> Tel: 0043 1 4277 61630, >> Fax: 0043 1 4277 9616, >> e-mail: die...@me... >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > |
|
From: Jose M. de la R. T. <del...@gm...> - 2017-05-19 06:02:33
|
Dear Dieter, As Juha suggested, it would be better to use branch release-1.1, which is going to be the next official release. Juha, correct me if I'm wrong, but I think that localrec would need Relion 1.4, and currently does not work with 2.0. In Scipion, both versions can live together. Indeed, you don't need to modify your environment, Scipion will do it for you when launching Relion jobs (the same for other packages). It is also possible to reuse package installations (if the version is the one used in Scipion). You just need to create a symbolic link in the scipion/software/em folder with the proper name (package-version). Cheers, Jose Miguel On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen <ju...@st...> wrote: > Dear Dieter > > Please update your Scipion to 1.1 beta (balbino) from github branch > release-1.1-fixes. Localrec is part of that version and will be in the > official release 1.1 when that comes out. It is also compatible with Relion > 2.0. > > Best wishes, > Juha > > On 19 May 2017, at 08:14, Dieter Blaas <die...@me...> > wrote: > > Dear colleagues, > > I tried to install localrec in scipion (Scipion v1.0.1 > (2016-06-30) Augusto) following this instruction: > https://github.com/OPIC-Oxford/localrec/wiki/How-to-install but 'scipion > --help' does not show this software and 'scipion install localrec' does > not find it. > > 1) how do I install localrec? > > 2) once installed will it run also by using the latest relion version > (i.e. relion-2.0.x, which I have as a separate and independent install) > or do I have to use the old relion (v-1.4) and if so, can both version > live side by side (for example relion-1.4 within scipion and > relion-2.0.5 outside scipion? > > Thanks a lot for hints, > > Dieter > > > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Juha H. <ju...@st...> - 2017-05-19 05:32:10
|
Dear Dieter Please update your Scipion to 1.1 beta (balbino) from github branch release-1.1-fixes. Localrec is part of that version and will be in the official release 1.1 when that comes out. It is also compatible with Relion 2.0. Best wishes, Juha > On 19 May 2017, at 08:14, Dieter Blaas <die...@me...> wrote: > > Dear colleagues, > > I tried to install localrec in scipion (Scipion v1.0.1 > (2016-06-30) Augusto) following this instruction: > https://github.com/OPIC-Oxford/localrec/wiki/How-to-install but 'scipion > --help' does not show this software and 'scipion install localrec' does > not find it. > > 1) how do I install localrec? > > 2) once installed will it run also by using the latest relion version > (i.e. relion-2.0.x, which I have as a separate and independent install) > or do I have to use the old relion (v-1.4) and if so, can both version > live side by side (for example relion-1.4 within scipion and > relion-2.0.5 outside scipion? > > Thanks a lot for hints, > > Dieter > > > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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