Re: [galaxy-dev] Recently Used Histories
My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the Options button on the rightmost pane, Saved Histories in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. This seems useful if implemented well. I envision a drop-down below the 'saved histories' menu item that appears on extended hover and provides links to recent histories. To implement I suggest: (a) create a SQLAlchemy query of user's histories sorted by last update time with limit N (e.g., 5) (b) provide this list to the index.mako template in the root.py/index method (c) refresh the middle frame using handle_refresh_frames() code in message.mako To get started with Galaxy, you'll want to create a fork of galaxy-central and work locally. Once you have something that works, please issue a pull request. Thanks, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username
Hi guys, I got this working for a while, I have this in /misc/local/galaxy/galaxy-dist/lib/galaxy/jobs/rules/200_runners.py: def default_runner(user_email): username = user_email.split(@)[0] return drmaa://-V -pe batch 8 -A %s/ % username But lately user_email has started being passed in as None. Any ideas what might be causing that? Nothing has changed that I know of. Thanks, Greg On Thu, Mar 21, 2013 at 3:31 PM, greg margeem...@gmail.com wrote: Thanks John! I'll give it a try. I can't get to that link, it says forbidden. Do you have another way to access the content? What is the significance of the name 200_runners.py? Thanks! -Greg On Thu, Mar 14, 2013 at 12:43 PM, John Chilton chil...@msi.umn.edu wrote: Greg, I think you can do this with dynamic job runners. http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html Step 1) Set: default_cluster_job_runner = dynamic:///python/default_runner Step 2) Create the file `lib/galaxy/jobs/rules/200_runners.py`, with contents something like this: def default_runner(user_email): username = user_email.split(@)[0] return drmaa://-V -pe batch 8 -A %s/ % username and you should be good to go. -John On Wed, Mar 13, 2013 at 7:12 AM, greg margeem...@gmail.com wrote: Hi guys, I just wanted to check in and see if anyone had any ideas on this. (It's actually the -A flag I'm after.) I did try putting this in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/ I was thinking galaxy might substitute the user name for Account_Name but no luck :-( -Greg On Tue, Mar 12, 2013 at 1:42 PM, greg margeem...@gmail.com wrote: In our local galaxy install we want the cluster jobs to be run from the galaxy user but we want to include a -a [account name] to our grid software bills properly. Here's what I currently have in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8/ What I want is something like this: default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/ Is this possible? Thanks, Greg ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed bug related to readme files
Hello Lance, This issue should be corrected in change set 9994:f8cf776ff12f, which is currently running on both public tool sheds. Thanks for reporting this! Greg Von Kuster On Jun 12, 2013, at 6:25 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Lance, Thanks for the information - I'll have a fix out shortly. Greg Von Kuster On Jun 11, 2013, at 10:12 PM, Lance Parsons lpars...@princeton.edu wrote: I'm running the latest stable. The 500 error seems to be coming from the toolshed. Do you also get a 500 error at the toolshed URL in my previous message? There is nothing other than standard info line from the request in my pasted log. I'm not able to get to the log right now, but I'll send it once I get a chance tomorrow. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University Original message From: Greg Von Kuster g...@bx.psu.edu Date: 06/11/2013 10:00 PM (GMT-05:00) To: Lance Parsons lpars...@princeton.edu Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Toolshed bug related to readme files Hi Lance, What version of Galaxy are you running? Is the 500 error coming from your Galaxy server or the tool shed server? Can you send the relevant information from your Galaxy paster log when attempting to reinstall? Thanks, Greg Von Kuster On Jun 11, 2013, at 3:52 PM, Lance Parsons lpars...@princeton.edu wrote: I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard). When I attempt to reinstall (after successfully uninstalling) I get a 500 error. After a bit of poking around, it seems that this URL generates the 500 error: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picardowner=devteamchangeset_revision=e0232cbac965 Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] blastn: Error: NCBI C++ Exception
Hi guys, another error appeared after we installed NCBI BLAST + to our local Galaxy instance and wanted to test it. After uploading some testdata to our history we tried to run blastn on it and got the following error: Fatal error: Matched on Error: Error: NCBI C++ Exception: /opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp, line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. With some testing around we figure out the problem: ./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out ~/out2.txt -outfmt 6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen -num_threads 8 Doesn't work until we replaced the num_threads 8 like it is written in the original ncbi_blastn_wrapper.xml with num_threads 1 Editing the .xml also solved the problem within the galaxy surface. Now my question is, is there any other workaround without editing the ncbi_blastn_wrapper.xml? Searching in the documentation and the mailing list, I did not find anything about this. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
Hello, After the latest update of Galaxy I saw that the cuffdiff wrapper is for version 2.0. I updated the $PATH to cuffdiff v. 2.0.2 but when I run cuffdiff in Galaxy I get the following error: Error running cuffdiff. cuffdiff: /lib64/libz.so.1: no version information available (required by cuffdiff) cuffdiff: unrecognized option '--library-norm-method' cuffdiff v1.3.0 (3022) What else do I need to define inorder to run the latest version of cuffdiff. Thank you, Karen ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Blast+: new feature filter/mask... by taxid before job in one task
Hi guys, We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask ... by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be performed in one task. However searching in the documentation and the mailing list, I did not find anything about this. So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] database upgrade crashes after upgrade to the June 3, 2013 Galaxy release
Hi, Sorry to bother again, but we have now a problem with the last release of galaxy-dist The lack of a python module asked by a python eggs seems to interrupt our postgresql database upgrade from version '114' to '115' sh manage_db.sh upgrade Traceback (most recent call last): File ./scripts/manage_db.py, line 13, in module from migrate.versioning.shell import main File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py, line 12, in module from migrate.versioning import api File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py, line 33, in module from migrate.versioning import (repository, schema, version, File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py, line 13, in module from migrate.versioning import version, pathed, cfgparse File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py, line 10, in module from migrate.versioning import pathed, script File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py, line 11, in module from migrate.versioning.util import KeyedInstance File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py, line 7, in module from decorator import decorator ImportError: No module named decorator Any idea ? Thanks Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] blastn: Error: NCBI C++ Exception
Hi Thomas, which wrapper did you use, the one from the toolshed or testtoolshed? Can you have a look at that thread please? http://dev.list.galaxyproject.org/Blast-Errors-td4659419.html Hi guys, another error appeared after we installed NCBI BLAST + to our local Galaxy instance and wanted to test it. After uploading some testdata to our history we tried to run blastn on it and got the following error: Fatal error: Matched on Error: Error: NCBI C++ Exception: /opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26 +-src/c++/src/corelib/ncbiobj.cpp, line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. With some testing around we figure out the problem: ./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out ~/out2.txt -outfmt 6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen -num_threads 8 Doesn’t work until we replaced the “num_threads 8” like it is written in the original “ncbi_blastn_wrapper.xml” with “num_threads 1” Editing the .xml also solved the problem within the galaxy surface. Now my question is, is there any other workaround without editing the” ncbi_blastn_wrapper.xml”? Not yet, the infrastructure is still missing for such a feature, afaik. Sorry. Cheers, Björn Searching in the documentation and the mailing list, I did not find anything about this. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Blast+: new feature filter/mask... by taxid before job in one task
Hi Thomas, are you interested in implementing it on your own? I'm not an blast expert, so sorry for the question, but is there an public repository where all unit-counts can be download as wmasker.obinary format, preferable in the correct folder structure as described in http://www.ncbi.nlm.nih.gov/books/NBK1763/. Or do you need to create such files on your own? What we/you probably can do is to create a new windowmasker.loc file pointing to each taxid and add a that new parameter to the wrapper. Cheers, Björn Hi guys, We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask … by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be performed in one task. However searching in the documentation and the mailing list, I did not find anything about this. So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] database upgrade crashes after upgrade to the June 3, 2013 Galaxy release
Hi Christophe, can you try to update to the latest revision? It is fixed here: https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077facb54804576be49ca545d18bd4e Cheers, Bjoern Hi, Sorry to bother again, but we have now a problem with the last release of galaxy-dist The lack of a python module asked by a python eggs seems to interrupt our postgresql database upgrade from version '114' to '115' sh manage_db.sh upgrade Traceback (most recent call last): File ./scripts/manage_db.py, line 13, in module from migrate.versioning.shell import main File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py, line 12, in module from migrate.versioning import api File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py, line 33, in module from migrate.versioning import (repository, schema, version, File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py, line 13, in module from migrate.versioning import version, pathed, cfgparse File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py, line 10, in module from migrate.versioning import pathed, script File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py, line 11, in module from migrate.versioning.util import KeyedInstance File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py, line 7, in module from decorator import decorator ImportError: No module named decorator Any idea ? Thanks Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy Security Notification
A security vulnerability was recently discovered by Björn Grüning with Galaxy's user impersonation feature that can expose an administrator's active history to users whom they impersonate. Only Galaxy instances with `allow_user_impersonation = True` set in their configurations are affected, and only if an administrator makes use of the impersonation feature. By default, user impersonation is disabled. A fix (id: 9d42f1e32efb) has been provided in the stable branch of Galaxy. To apply the fix, ensure you are on the stable branch and upgrade to the latest changeset: % hg branch stable % hg pull -u For Galaxy installations on relatively old versions that administrators are not yet ready to upgrade, there are three workarounds. First, the patch can be downloaded and applied manually: % wget -o security.patch https://bitbucket.org/galaxy/galaxy-central/commits/9d42f1e32efb654fda1e011dc66a4aa5888717f1/raw/ and then: % hg patch security.patch or: % patch -p1 security.patch Second, the impersonation feature can be disabled by setting the following option in Galaxy's configuration file: allow_user_impersonation = False In all of the above cases, the Galaxy server process(es) must be restarted for the change to take effect. Third, the feature can be left enabled and unpatched, and the vulnerability can be worked around by educating administrators who use the feature. As long as a new history is created by the administrator prior to switching to the impersonated user, no data will be exposed to the impersonated user. --nate Galaxy Team ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version
Hello, After the latest update of Galaxy I saw that the cuffdiff wrapper is for version 2.0. I updated the $PATH to cuffdiff v. 2.0.2 but when I run cuffdiff in Galaxy I get the following error: Error running cuffdiff. cuffdiff: /lib64/libz.so.1: no version information available (required by cuffdiff) cuffdiff: unrecognized option '--library-norm-method' cuffdiff v1.3.0 (3022) What else do I need to define inorder to run the latest version of cuffdiff. This depends on your setup. If you're running Galaxy under a particular user, you may have to update that user's $PATH. If you're running on a cluster, you'll need to ensure that the submission script uses the correct $PATH. If you provide more details on your set up, it may be possible to provide additional insight/suggestions for your problem. Best, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] blastn: Error: NCBI C++ Exception
On 06/12/2013 04:06 PM, Berner, Thomas wrote: Hi guys, another error appeared after we installed NCBI BLAST + to our local Galaxy instance and wanted to test it. After uploading some testdata to our history we tried to run blastn on it and got the following error: Fatal error: Matched on Error: Error: NCBI C++ Exception: /opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp, line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. With some testing around we figure out the problem: ./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out ~/out2.txt -outfmt 6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen -num_threads 8 Doesn't work until we replaced the num_threads 8 like it is written in the original ncbi_blastn_wrapper.xml with num_threads 1 Editing the .xml also solved the problem within the galaxy surface. Now my question is, is there any other workaround without editing the ncbi_blastn_wrapper.xml? You can recompile blast+ enabling multithreading (--with-mt option) -- Mauro ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] database upgrade crashes after upgrade to the June 3, 2013 Galaxy release
Thank you so much Björn, I made the change of the file directly by hand (not sure to be able to cleanly switch to default from stable with the new mercurial mode) and it worked. Chris 2013/6/12 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de Hi Christophe, can you try to update to the latest revision? It is fixed here: https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077facb54804576be49ca545d18bd4e Cheers, Bjoern Hi, Sorry to bother again, but we have now a problem with the last release of galaxy-dist The lack of a python module asked by a python eggs seems to interrupt our postgresql database upgrade from version '114' to '115' sh manage_db.sh upgrade Traceback (most recent call last): File ./scripts/manage_db.py, line 13, in module from migrate.versioning.shell import main File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py, line 12, in module from migrate.versioning import api File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py, line 33, in module from migrate.versioning import (repository, schema, version, File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py, line 13, in module from migrate.versioning import version, pathed, cfgparse File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py, line 10, in module from migrate.versioning import pathed, script File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py, line 11, in module from migrate.versioning.util import KeyedInstance File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py, line 7, in module from decorator import decorator ImportError: No module named decorator Any idea ? Thanks Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] database upgrade crashes after upgrade to the June 3, 2013 Galaxy release
Christophe, Glad it's working. The updates should merge seamlessly so you shouldn't need to do anything else when you update again. That said, for future use, you can swap branches like: 'hg update stable' to swap to the stable branch. If you're on galaxy-dist, you can still pull (and update) from the stable branch in galaxy-central using 'hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central'. -Dannon On Wed, Jun 12, 2013 at 5:33 PM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Thank you so much Björn, I made the change of the file directly by hand (not sure to be able to cleanly switch to default from stable with the new mercurial mode) and it worked. Chris 2013/6/12 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de Hi Christophe, can you try to update to the latest revision? It is fixed here: https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077facb54804576be49ca545d18bd4e Cheers, Bjoern Hi, Sorry to bother again, but we have now a problem with the last release of galaxy-dist The lack of a python module asked by a python eggs seems to interrupt our postgresql database upgrade from version '114' to '115' sh manage_db.sh upgrade Traceback (most recent call last): File ./scripts/manage_db.py, line 13, in module from migrate.versioning.shell import main File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py, line 12, in module from migrate.versioning import api File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py, line 33, in module from migrate.versioning import (repository, schema, version, File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py, line 13, in module from migrate.versioning import version, pathed, cfgparse File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py, line 10, in module from migrate.versioning import pathed, script File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py, line 11, in module from migrate.versioning.util import KeyedInstance File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py, line 7, in module from decorator import decorator ImportError: No module named decorator Any idea ? Thanks Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
