Re: [galaxy-dev] user names with authentication
This is great! I'll try it out early next week, but its good to know someone else is interested in the same feature. From: Adam Brenner [aebre...@uci.edu] Sent: Friday, April 19, 2013 12:42 AM To: John Chilton Cc: Jillian Rowe; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user names with authentication John, that worked! I was able to upload some sample files using usernames, rather then full email address. No errors, no bugs. Thanks! -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/http://www.ics.uci.edu/~aebrenne/ aebre...@uci.edumailto:aebre...@uci.edu On Thu, Apr 18, 2013 at 2:18 PM, John Chilton chil...@msi.umn.edumailto:chil...@msi.umn.edu wrote: Crazy coincidence, I had the same problem and hadn't even seen the original e-mail from Jillian. My pull request implementing this was merged by Nate earlier this week. https://bitbucket.org/galaxy/galaxy-central/pull-request/157/increased-flexibility-for-ftp-directory/diff You can just grab the three changesets out of there and apply them to your local galaxy repository. Then you just need to set the new `ftp_upload_dir_identifier` option in universe_wsgi.ini to `username`. Hope this helps. -John On Thu, Apr 18, 2013 at 4:07 PM, Adam Brenner aebre...@uci.edumailto:aebre...@uci.edu wrote: We would also be looking forward to seeing a solution (or hack) like this. We currently have a a gluster filesystem setup where users drop big data to /gl/tmp/user/. Keeping this format would be best. However, I believe a simple symbolic link would also work with Galaxy. for i in $(ls /gl/tmp/user); do ln -s /gl/tmp/user /gl/tmp/u...@uci.edumailto:u...@uci.edu;done; -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/http://www.ics.uci.edu/~aebrenne/ aebre...@uci.edumailto:aebre...@uci.edu On Sun, Apr 14, 2013 at 1:12 AM, Jillian Rowe jir2...@qatar-med.cornell.edumailto:jir2...@qatar-med.cornell.edu wrote: Hello, I have a galaxy instance authentication using LDAP. The authentication works fine, and I would like to enable the user upload option. I would like to have: user_library_import_dir = /a/path and for galaxy to look for users with just the username. So if I log in with au...@example.commailto:au...@example.com I want for galaxy to look in /a/path/auser instead of /a/path/au...@example.commailto:au...@example.com Is there anywhere I can set this? Best, Jillian ___ 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] Step 3 of get Microbial Data install
Hello, I try to set Get Microbial Data in my local instance of Galaxy. So, as explain in /path/to//src/galaxy/galaxy-dist/scripts/microbes/README.txt , step 1 and 2 or OK, binary 'faToNib' is available on our cluster, but step 3 generate empty files : drwxr-xr-x 4 galaxy wbioinfo 100 18 avril 14:26 .. -rw-r--r-- 1 galaxy wbioinfo 203 18 avril 14:26 harvest.txt -rw-r--r-- 1 galaxy wbioinfo 69 18 avril 14:34 ncbi_to_ucsc.txt -rw-r--r-- 1 galaxy wbioinfo 0 19 avril 15:47 sequence.txt -rw-r--r-- 1 galaxy wbioinfo 0 19 avril 15:47 seq.loc drwxr-xr-x 2 galaxy wbioinfo 118 19 avril 15:47 . Could you please, hel me ? Thnaks in advance, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ 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-user] Question about scripting
Hello, I've moved this over to the galaxy-dev list since it concerns a local installation. You'll want to use the 'condor' job running plugin, which is provided with the Galaxy distribution. Have a look at the job_conf.xml.sample_advanced file to see how this would be configured. A very basic job_conf.xml that should submit all jobs to HTCondor: ?xml version=1.0? job_conf plugins workers=4 plugin id=condor type=runner load=galaxy.jobs.runners.condor:CondorJobRunner / /plugins destinations default=condor destination id=condor runner=condor/ /destinations /job_conf --nate On Apr 19, 2013, at 8:32 AM, leconte wrote: hello, My subject is at the border between Galaxy and Condor I'found method to use Galaxy with condor cluster solution. In fact I have wrote a script when Galaxy call clustalw2 , it calls in fact a script called clustalw2. All run exactly as I want excepting ... but Galaxy get in error and said there was a problem I turn my script to debug mode and it puts followings output + prog=/usr/bin/clustalw2 + err=0 + infile=-infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat + outfile=-outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat + outorder=-OUTORDER=ALIGNED + seqnos=-SEQNOS=OFF + typeseq=-TYPE=DNA + var6= + var7= + var8= + var9= + echo ++ echo -infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat ++ sed -e s/-infile=// + infile2=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat ++ sed -e 's/galaxy_dataset_\(.*\)\.dat//' ++ sed -e s/-outfile=// ++ echo -outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat + WorkingDir=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/ + mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/ + mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/ + mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/ + [[ -n /usr/bin/clustalw2==clustalw2 ]] + echo 'universe= vanilla' + echo 'executable = /usr/bin/mpirun ' + echo 'arguments = -np 10 -hostfile /home/galaxy/hostfile /usr/bin/clustalw-mpi -infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat -outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat -OUTORDER=ALIGNED -SEQNOS=OFF -TYPE=DNA ' + echo 'Getenv = True machine_count = 1 transfer_input_files= /home/galaxy/hostfile,/usr/bin/clustalw-mpi, /home/galaxy/galaxy-dist/database/files/000/dataset_11.dat should_transfer_files = yes Log = /home/galaxy/logs/normal.$(cluster).$(process).log Output = /home/galaxy/logs/normal.$(cluster).$(process).out Error = /home/galaxy/logs/normal.$(cluster).$(process).error notification= never queue 1' + /usr/bin/condor_submit /home/galaxy/submit Submitting job(s). 1 job(s) submitted to cluster 179. I suspect the method I use, doesn't return properly information to galaxy ... but I don't know what I can do ... Any Idea ... ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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] traceback - local error?
172.17.130.203 - - [19/Apr/2013:10:31:20 -0400] GET /api/datasets/dd61915e24aa3fd0?hda_ldda=hdadata_type=converted_datasets_statechrom=chr1 HTTP/1.1 200 - http://galaxy.neb.com/visualization/trackster?dataset_id=b8edc02014d74addhda_ldda=hda; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_3) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.65 Safari/537.31 galaxy.webapps.galaxy.api.datasets ERROR 2013-04-19 10:31:21,775 Error in dataset API at listing contents: unpack requires a string argument of length 4: unpack requires a string argument of length 4 Traceback (most recent call last): File /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 41, in show is_true( kwd.get( 'retry', False ) ) ) File /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 1037, in has_data f, bbi = self._get_dataset() File /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 1170, in _get_dataset return f, BigWigFile(file=f) File bigwig_file.pyx, line 127, in bx.bbi.bigwig_file.BigWigFile.__init__ (lib/bx/bbi/bigwig_file.c:3011) File bbi_file.pyx, line 119, in bx.bbi.bbi_file.BBIFile.__init__ (lib/bx/bbi/bbi_file.c:3508) File bbi_file.pyx, line 129, in bx.bbi.bbi_file.BBIFile.open (lib/bx/bbi/bbi_file.c:3660) File /mnt/ngswork/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg/bx/misc/binary_file.py, line 30, in __init__ if struct.unpack( I, bytes )[0] == magic: error: unpack requires a string argument of length 4 Is this a bug or have I done something unexpected? I'm trying to use the trackbrowser to visualize some bam files that I aligned to a genome that I had to install manually (Zea_mays_B73_RefGen_v2), maybe i've screwed something up. I was initially able to see some reads, but after reverting to the sample datatypes file and restarting galaxy i can't see anything anymore. I also added a .2bit file to twobit.locs Zea_mays_AGPv2 /mnt/ngswork/galaxy/galaxy-dist/tool-data/genome/Zea_mays_AGPv2/seq/Zea_mays_AGPv2.2bit maybe that's related... I've tried copying the bams to a new history - and they seem to be reindexing as a result, but I still see no reads. Any ideas? Brad -- Brad Langhorst langho...@neb.commailto:langho...@neb.com ___ 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] TestToolShed out of date? (not running unit tests)
Peter, I've committed a fix for this in 9480:a80175a97194, and re-run the automated testing framework. However, as you will see, the test still reports an error. This is not due to an issue in your repository, but an problem on the Galaxy side, as described in the following trello card: https://trello.com/c/KdGX3hkh --Dave B. On 4/17/13 06:20:39.000, Peter Cock wrote: On Wed, Apr 17, 2013 at 9:44 AM, Peter Cock p.j.a.c...@googlemail.com mailto:p.j.a.c...@googlemail.com wrote: On Tue, Apr 16, 2013 at 9:42 PM, Greg Von Kuster g...@bx.psu.edu mailto:g...@bx.psu.edu wrote: Hello Peter, On Apr 15, 2013, at 11:04 AM, Peter Cock wrote: The View tool functional test results option clearly lists failed tests, but it is not obvious if there were any successful tests. Could that be indicated somehow (e.g. five tests passed for tool xxx). Here's a problem case, http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr This has one unit test defined, tests test param name=blastxml_file value=blastp_four_human_vs_rhodopsin.xml ftype=blastxml / param name=topN value=3 / output name=tabular_file file=blastp_four_human_vs_rhodopsin_top3.tabular ftype=tabular / /test /tests However, it is not shown via View tool functional test results: Tool functional test results Time tested: ~ 6 hours ago *Tool Shed environment* Tool shed version: 9252:da2d6ee29f30 Tool shed database version: 17 Mercurial version: 2.2.3 *Galaxy environment* Galaxy version: unknown Galaxy database version: unknown Architecture: x86_64 Operating system: Linux 3.0.0-1-amd64 Python version: 2.7.2+ i.e. No mention of the fact there was (presumably) one successful test. Peter ___ 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] TestToolShed out of date? (not running unit tests)
On Fri, Apr 19, 2013 at 4:46 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I've committed a fix for this in 9480:a80175a97194, and re-run the automated testing framework. However, as you will see, the test still reports an error. This is not due to an issue in your repository, but an problem on the Galaxy side, as described in the following trello card: https://trello.com/c/KdGX3hkh --Dave B. Thanks - once this and the best way forward for defining Python modules as dependencies are sorted out I should be able to get more of my tools in the Tool Shed passing their unit tests :) Peter ___ 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 functional tests bug
Peter, Again, thank you for reporting this issue, I've committed a fix in 9470:d056556a1e63 and re-run the testing framework, and the functional test results page now shows the data for the tmhmm_and_signalp repository only. --Dave B. On 4/16/13 16:47:25.000, Greg Von Kuster wrote: Hello Peter, Thanks for reporting this - I've created the following Trello card for this issue. We'll get this fixed asap. https://trello.com/card/toolshed-automated-functional-test-bug/506338ce32ae458f6d15e4b3/793 Greg Von Kuster On Apr 15, 2013, at 11:21 AM, Peter Cock wrote: On Thu, Apr 4, 2013 at 9:47 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I've been looking at the new functional test results now being shown on the tool shed, and found a bug/glitch: 1. Goto http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 2. Click on top right menu Repository Actions, View functional test results menu item 3. Notice two failed tests for htseq_count (which is not in this repo) This was for 12:6753a9261390 of this repo. Peter This bug is also happening on the Test Tool Shed, e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp Peter ___ 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] Errors when starting galaxy
Dear all, I get the following errors when starting galaxy, is there any way to fix this. Error loading display application (./display_applications/genetrack.xml): [Errno 2] No such file or directory: './display_applications/genetrack.xml' Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 498, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py, line 163, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) Error loading display application (./display_applications/genetrack.xml): [Errno 2] No such file or directory: './display_applications/genetrack.xml' Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 498, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py, line 163, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) Best, --Ricardo Perez ___ 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] Any hint on how to use Galaxy within virtualenv?
Jean-Francois, Are you running a current revision of Galaxy? This issue should be resolved in recent galaxy releases. -Dannon On Fri, Apr 19, 2013 at 3:47 PM, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca wrote: Dear Galaxy mailing list, We ran into the same issue described in this post: http://dev.list.galaxyproject.org/markupsafe-module-conflicts-tc4656214.html The exact error message we are getting, with a few different tools is: /Galaxy/galaxy_dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but /Galaxy/galaxy_dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() From the solution given in the above-mentioned post, I guess we would have to run Galaxy inside virtualenv. (Details of the procedure to install virtualenv, are given here: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer) However, I am not sure to understand completely how it works. Can we use our already existing Galaxy instance with virtualenv? And how can we achieve this? For the installation of virtualenv part, I think we are ok. It is the next step: how to tell Galaxy to run in this virtualenv, that I am not sure about. Thank you in advance for your help! *Jean-Francois* ___ 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/
