January 2013 - galaxy-dev - lists.galaxyproject.org

show urls in csv (in eye mode)
by Hagai Cohen 20 Mar '13

20 Mar '13

Hi, I have a tool which outputs a csv file with links. When I press the eye icon - I would like these links to be shown as links in the browser. It is possible? Thanks, Hagai

2 5

Updating help text for a tool shed repository
by Lance Parsons 11 Mar '13

11 Mar '13

I recently updated the htseq-count tool in the Galaxy toolshed to version 0.3. This version has some functional changes and thus the tool version was incremented. I installed this new version of the tool in my local Galaxy instance. However, I realized later that I missed updating one part of the help text. Today I fixed that text (but left the tool version the same), tarred up the file, and uploaded it to the toolshed. I then attempted to "Get Updates" from my local Galaxy instances for that tool got the following error: URL: http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision… File '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 206 in decorator return func( self, trans, *args, **kwargs ) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1677 in update_to_changeset_revision update_repository( repo, latest_ctx_rev ) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py', line 1428 in update_repository rev=ctx_rev ) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py', line 5661 in update rev = scmutil.revsingle(repo, rev, rev).rev() File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 515 in revsingle l = revrange(repo, [revspec]) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 588 in revrange for r in m(repo, range(len(repo))): File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 1414 in mfunc return getset(repo, subset, tree) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 156 in getset return methods[x[0]](repo, subset, *x[1:]) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 171 in symbolset return stringset(repo, subset, x) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 161 in stringset x = repo[x].rev() File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py', line 235 in __getitem__ return context.changectx(self, changeid) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py', line 103 in __init__ _("unknown revision '%s'") % changeid) RepoLookupError: unknown revision '11' I believe this is because the revision I have installed (10) is not longer considered a valid revision by the toolshed (I presume since it is an older revision of with the same tool version). Any help would be appreciated. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

4 9

Please help with fastx broken pipe
by Jorge Sepulveda 07 Mar '13

07 Mar '13

Hi, Fresh new installation of galaxy on a MacPro 12 core Mountain Lion Trying to run fastx_quality_stats: galaxy.jobs.manager DEBUG 2013-01-16 16:03:49,646 (7) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-01-16 16:03:54,759 (7) Working directory for job is: /Users/JS/galaxy-dist/database/job_working_directory/000/7 galaxy.jobs.handler DEBUG 2013-01-16 16:03:54,759 dispatching job 7 to local runner galaxy.jobs.handler INFO 2013-01-16 16:03:54,854 (7) Job dispatched galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:54,919 Local runner: starting job 7 galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,198 executing: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat' galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,396 execution finished: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat' galaxy.jobs DEBUG 2013-01-16 16:03:55,440 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-01-16 16:03:55,496 setting dataset state to ERROR galaxy.tools DEBUG 2013-01-16 16:03:55,618 Error opening galaxy.json file: [Errno 2] No such file or directory: '/Users/JS/galaxy-dist/database/job_working_directory/000/7/galaxy.json' galaxy.jobs DEBUG 2013-01-16 16:03:55,679 job 7 ended 127.0.0.1 - - [16/Jan/2013:16:03:59 -0400] "GET /history HTTP/1.1" 200 - "http://127.0.0.1:8080/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" Galaxy reports the following error: /bin/sh: fastx_quality_stats: command not found cat: stdout: Broken pipe When run on the cmd line, it runs fine: $ cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_6.dat' $ more /Users/JS/galaxy-dist/database/files/000/dataset_6.dat column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count 1 912999 7 46 31022469 33.98 32 35 37 5 25 44 153534 361457 322516 75492 0 912999 2 912999 3 46 29744797 32.58 31 34 36 5 24 43 316245 255564 197711 143479 0 912999 Jorge Sepulveda, MD, PhD Associate Director for Laboratory Medicine, Medical Director of Laboratory Informatics, Columbia University Medical Center Associate Professor, Department of Pathology & Cell Biology Columbia University College of Physicians and Surgeons PH1590B 622 W 168 St New York, NY 10032 Cell: (917) 862-6050 Office: 212-305-6360 E-mail:jls2282@columbia.edu

2 1

Composite datatype output for Cuffdiff
by Jim Johnson 06 Mar '13

06 Mar '13

Checking to see if there is any interest in including a parameter option to select outputs for cuffdiff, potentially including a composite output and a cummeRbund sqlite database. Issues: cuffdiff produces 21 output files, which is a little unwieldy in a galaxy history. cummeRbund generates its database when given a cuffdiff output directory, but manually hooking up 21 outputs to the cummerbund_wrapper is a pain. I've put demo code in the testtoolshed under the name repository name cummerbund http://jjohnson@testtoolshed.g2.bx.psu.edu/repos/jjohnson/cummerbund This includes new datatypes defined in datatypes_conf.xml and implemented in cuffdata.py:  <datatype extension="cuffdata" type="galaxy.datatypes.cuffdata:CuffDiffData"/>  <datatype extension="cuffdatadb" type="galaxy.datatypes.cuffdata:CuffDataDB"/> The cuffdiff wrapper has a multiple select parameter to choose which output files to put in the history. In addition to the 21 cuffdiff outputs, the wrapper can also generate: cuffdata - which is a composite HTML output with links to the 21 cuffdiff outputs cuffdatadb - which is the cummeRbund SQLite database I also added utility tools: cuffdata_datasets - which will take files from the composite cuffdata and copy them as datasets into the history cuffdata_cummerbund - which generates the cummeRbund cuffdatadb from the composite cuffdata I updated the cummerbund_wrapper: with tryCatch so that a R error on a plot won't exit the Rscript to include a small image of each plot on the html page added plots for : dispersion, scatter matrix, MDS, and PCA Thanks, JJ

7 10

Bug in handling user job limits
by Lance Parsons 04 Mar '13

04 Mar '13

I submitted a trello "ticket" [(https://trello.com/c/6vxkqdjT) regarding this, but wanted to make sure I brought it to someone's attention (it's causing me some queue issues with my instance of galaxy). When registered_user_job_limit and anonymous_user_job_limit are set in universe.wsgi jobs cannot be run, instead the following error occurs: galaxy.jobs.handler ERROR 2012-12-04 12:44:51,869 failure running job 22396 Traceback (most recent call last): File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 183, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 253, in __check_if_ready_to_run state = self.__check_user_jobs( job ) File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 274, in __check_user_jobs if not self.user_job_count: AttributeError: 'JobHandlerQueue' object has no attribute 'user_job_count' Commenting out the lines for registered_user_job_limit and anonymous_user_job_limit in universe.wsgi allows job to be queue one again. It looks like this is due to the fact that `self.__clear_user_job_count()` on line 159 of `handler.py` is only called when jobs are tracked in the database. If jobs are not tracked in the database (as in my case), the error occurs. Perhaps the fix would be to simply move the call outside the `if` block. It appears this was broken in the 2012-11-13 revision (73e05bc). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

3 5

macs error for chipseq data
by Jennifer Jackson 01 Mar '13

01 Mar '13

Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: > > Hi Jen, > > Sorry that I missed some part of your email. It is not for local > galaxy install. I am using the cloudman from aws and it seemed to have > everything for having the input files and reference genome chose. The > job was shown on the right panel and then the error message coming out. > > It seems to me that MACS was installed.... What is the issue? > > Thank you very much, > > Kathryn > On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: > > Hi Jennifer, > > Thanks for the information on MACS tools. > > Yes, I forgot to mention that I used bowtie mapped files as the input. > > Thank you very much, > > Kathryn > > ** > > *From:*Jennifer Jackson [mailto:jen@bx.psu.edu] > *Sent:* Friday, January 11, 2013 3:48 AM > *To:* Sun, Wenping [USA] > *Cc:* galaxy-user(a)bx.psu.edu > *Subject:* [External] Re: [galaxy-user] macs error for chipseq data > > Hello Kathryn, > > This is occurring on your local Galaxy install? Have you installed the > actual MACS tool and set up the proper configuration paths? Details > for how to do this are in these wikis: > http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies > > Apart from that, I should let you know that prior to running MACS, > groomed fastq datasets first need to be mapped. An example can be > found in our Using Galaxy paper, protocol #3. Links to the paper and > supplemental materials (including a screencast walk-through) are > available here: > https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 > > If you need more help with your local install, directing questions to > the galaxy-dev(a)bx.psu.edu <mailto:galaxy-dev@bx.psu.edu> mailing list > would be best, > > Thanks! > > Jen > Galaxy team > > On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: > > Dear galaxy users, > > I've encountered the error while running macs on galaxy for > chipseq data. I used fastq groomed files as input and had the > following error > > An error occurred running this job: //bin/sh: macs: not found/ > > // > > Anybody can kindly provide some hints? > > Thanks, > > Kathryn > > > > > ___________________________________________________________ > > 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/ > > > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

6 10

Downloading datasets without username/password when login is required
by Sytchev, Ilya 26 Feb '13

26 Feb '13

Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya

2 3

Tabular file metadata - columns names
by Peter 22 Feb '13

22 Feb '13

Hi all, I'd like to know more about Galaxy's column metadata for tabular files. In the workflow editor under "Edit Step Actions" you can pick "Assign Columns", and then give column numbers for five predefined cases: Chrom, Start, End, Strand, Name. Do these "named columns" get shown anywhere in the Galaxy UI? For example, in a column select parameter widget? Is it possible to assign these columns in a tool's wrapper XML file? >From http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax I'm aware of the metadata_source attribute to *copy* the meta data from the input file, but that isn't always relevant. Can I somehow specify that my tool has tabular output where column 1 is "Name"? Is it possible to introduce additional column types? e.g. "evalue" or "Description". Thanks, Peter

3 7

environment variables and paths for toolshed tools
by David Hoover 20 Feb '13

20 Feb '13

Are there any environment variables that are honored by toolshed installed tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or $GALAXY_HOME, then uploaded it the test toolshed, then installed it automatically. Neither of these resolved to what I expected. I don't want to hard-code the path in the xml tool file, but rather have a default location for other executables and jar files. How should this best be done? David Hoover Helix Systems Staff

3 14

changing datasets file_path storage location
by Shantanu Pavgi (Campus) 19 Feb '13

19 Feb '13

We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed? -- Thanks, Shantanu

3 4