[galaxy-dev] ebio_deseq tool error
Hello,
I installed 'ebio_deseq' tool via Admin/Tool sheds, and I am getting this
error (looks like someting is making R plotting code unhappy).
Error running DESeq analyse: Error in if (!ok) warning("some notches went
outside hinges ('box'): maybe set notch=FALSE") :
missing value where TRUE/FALSE needed
Calls: PlotViolin ... boxplot.matrix -> boxplot -> boxplot.default ->
do.call -> bxp
Execution halted
I would be grateful for help or suggestions for addressing this issue.
thanks,
Sergei
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[galaxy-dev] Galaxy with Rocks Cluster / Submitting Job As Real User
Hi, I've been trying to get Galaxy to submit jobs to my cluster as the "real user" rather than the "galaxy" user. In my galaxy.ini, I have: outputs_to_working_directory = True set_metadata_externally = True drmaa_external_runjob_script = /galaxy/scripts/drmaa_external_runner.py drmaa_external_killjob_script = /galaxy/scripts/drmaa_external_killer.py drmaa_external_chown_script = /galaxy/scripts/external_chown_script.py In my sudoers file I have: galaxy ALL= (root) NOPASSWD: SETENV: /galaxy/scripts/drmaa_external_runner.py galaxy ALL= (root) NOPASSWD: SETENV: /galaxy/scripts/drmaa_external_killer.py galaxy ALL= (root) NOPASSWD: SETENV: /galaxy/scripts/external_chown_script.py In my log file, I'm seeing: galaxy.jobs.runners.drmaa DEBUG 2014-10-29 14:45:54,777 (15) submitting file /galaxy/database/job_working_directory/000/15/galaxy_15.sh galaxy.jobs.runners.drmaa DEBUG 2014-10-29 14:45:54,783 (15) submitting with credentials: tjg [uid: 28369] galaxy.jobs.runners ERROR 2014-10-29 14:45:54,784 (15) Unhandled exception calling queue_job Traceback (most recent call last): File "/galaxy/lib/galaxy/jobs/runners/__init__.py", line 96, in run_next method(arg) File "/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 189, in queue_job filename = self.store_jobtemplate(job_wrapper, jt) File "/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 348, in store_jobtemplate f = open(filename,'w') IOError: [Errno 2] No such file or directory: '/galaxy/database/pbs/15.jt_json' My /var/log/messages file is not reporting any attempt to run "sudo", so I think the process is failing before it gets to that point in the Galaxy code. If I comment out the "drmaa_external_*" lines, the jobs are submitted successfully and run as the "galaxy" user. What am I missing here? :) -- Tim Gustafson t...@ucsc.edu 831-459-5354 Baskin Engineering, Room 313A ___ 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] Stop autoselecting in drop-down menus
On Wed, Oct 29, 2014 at 7:45 AM, Aleksey Jironkin < aleksey.jiron...@phe.gov.uk> wrote: > > Hi, > > I was wondering if there is a way to prevent auto-selecting an option > for Running a workflow? Quiet often users (especially novices) would > re-run workflows without checking much the data that goes in thinking it > will be the same as before. But because the options in drop down menus > are auto-populated it seems the top option is always selected by > default. For example, previously we had a single fasta file as reference > and in the process of a workflow few other fasta files get generated. > they appear above the previous fasta in the selection, so without paying > attention people skip the input without really checking it. This behavior would be a bug - workflow parameters should be preserved. What release are you on - we fixed a bug related to this after the initial August release ( https://bitbucket.org/galaxy/galaxy-central/commits/5abd9fc76f7ad2eca013a1f81a77a4d3fe28328a) that should be available in the latest august stable tag. Is it possible you were on the August release but don't have this fix? If it is a bug and is still present in the latest stable branch if you could provide steps to reproduce it in a clean clone of Galaxy it could go a long way toward helping us track down a fix. -John > > > Can we manually add a "blank" selection at the top to force users to > select something? > > > > Alex > > > -- > Dr Aleksey Jironkin > > Bioinformatician > Bioinformatics Unit > Infectious Disease Informatics > Microbiologicy Services, Colindale > Public Health England > 61 Colindale Avenue > London > NW9 5EQ > > aleksey.jiron...@phe.gov.uk > > Tel: 020 83 276610 > > www.gov.uk/phe Follow us on Twitter @PHE_uk > > Protecting and improving the nation’s health > > > > ___ > 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] Test failure, JSONDecodeError: Unpaired high surrogate
Hi all, I'm getting the following exception in a failing unit test: https://travis-ci.org/peterjc/pico_galaxy/builds/39398677 Testing this tool (where two of the three near identical tests passed): https://github.com/peterjc/pico_galaxy/blob/dd03346710e6a46cb6ec9dda1eed23d5fd301d03/tools/mummer/mummer.xml ``` Traceback (most recent call last): File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py", line 116, in test_tool self.do_it( td ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py", line 35, in do_it self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py", line 75, in _verify_outputs galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py", line 89, in verify_output self._verify_metadata( history_id, hid, attributes ) File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py", line 102, in _verify_metadata dataset = self._get( "histories/%s/contents/%s" % ( history_id, hid ) ).json() File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/eggs/requests-2.2.1-py2.7.egg/requests/models.py", line 740, in json return json.loads(self.content.decode(encoding), **kwargs) File "/usr/lib/python2.7/dist-packages/simplejson/__init__.py", line 413, in loads return _default_decoder.decode(s) File "/usr/lib/python2.7/dist-packages/simplejson/decoder.py", line 402, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/lib/python2.7/dist-packages/simplejson/decoder.py", line 418, in raw_decode obj, end = self.scan_once(s, idx) JSONDecodeError: Unpaired high surrogate: line 1 column 785 (char 785) ``` Probably relevant: - https://github.com/simplejson/simplejson/issues/62 - http://bugs.python.org/issue11489 Any thoughts? What does Galaxy write to these job-associated JSON metadata files? Thanks, 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/
[galaxy-dev] Stop autoselecting in drop-down menus
Hi, I was wondering if there is a way to prevent auto-selecting an option for Running a workflow? Quiet often users (especially novices) would re-run workflows without checking much the data that goes in thinking it will be the same as before. But because the options in drop down menus are auto-populated it seems the top option is always selected by default. For example, previously we had a single fasta file as reference and in the process of a workflow few other fasta files get generated. they appear above the previous fasta in the selection, so without paying attention people skip the input without really checking it. Can we manually add a "blank" selection at the top to force users to select something? Alex -- Dr Aleksey Jironkin Bioinformatician Bioinformatics Unit Infectious Disease Informatics Microbiologicy Services, Colindale Public Health England 61 Colindale Avenue London NW9 5EQ aleksey.jiron...@phe.gov.uk Tel: 020 83 276610 www.gov.uk/phe Follow us on Twitter @PHE_uk Protecting and improving the nation’s health signature.asc Description: This is a digitally signed message part ___ 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/
