galaxy-dev February 2013

galaxy-dev@lists.galaxyproject.org

113 participants
204 discussions

user creation using API
by Hagai Cohen 06 May '13

06 May '13

Hi, I would like to auto create users on my local Galaxy instance. I saw that in the "create user" on the API, I should enable use_remote_user (which as I understand means that I have to use Apache or nginx). Is there another way besides using Apache to create users automatically? Thanks, Hagai

3 3

ASN.1 (text and binary) formats in Galaxy & Tool Shed
by Peter Cock 02 May '13

02 May '13

Hello all, Although they are these days also offering XML for many tools, the NCBI still make heavy use of the older ASN.1 file format (both as plain text and binary). This crops up in BLAST (e.g. as the BLAST archive format, or as dustmasker output), in the Entrez Utilities (e.g. for sequence data as an alternative to GenBank for FASTA format etc, or pubmed, etc) and also for 3D structures. I think it could make sense to define generic 'asn1' and 'asn1-binary' formats in the Galaxy core (name suggestions welcome), and even perhaps 'ncbi-asn1' and 'ncbi-asn1-binary' too. Then ToolShed entries can define domain specific subclasses. For instance, the BLAST+ wrapper could include definitions for the dustmasker output, and perhaps the BLAST archive format too. Separately anyone working with 3D structures as ASN.1 could define another sub-format, etc. I see this as a clear analogy to the assorted XML file formats in existence - defined in Galaxy as subclasses of the core XML format included with the Galaxy core. Would a pull request implementing this be acceptable? Peter P.S. Does anyone know an authoritative source for the MIME types used by the NCBI? Using the BLAST website they offer plain text ASN.1 just as text/plain, likewise efetch also seems to use text/plain for ASN.1 downloads. However I've seen references to chemical/ncbi-asn1-ascii and chemical/ncbi-asn1-binary mime-types mentioned, e.g. http://www.ncbi.nlm.nih.gov/data_specs/asn/NCBI_all.asn i.e. It appears that 3D structure NCBI ASN.1 files use a well defined MIME type, while most NCBI ASN.1 text files default to text/plain - which we can handle nicely in Galaxy as subclasses.

4 10

Galaxy hg repository problem "abort: path ... traverses symbolic link"
by Peter Cock 29 Apr '13

29 Apr '13

Hi all, I've got an hg puzzle, can anyone on the Galaxy team explain the cause of this and what action I can take to avoid it? Starting with a clean checkout, $ hg clone https://bitbucket.org/galaxy/galaxy-central warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) destination directory: galaxy-central requesting all changes adding changesets adding manifests adding file changes added 8886 changesets with 33822 changes to 6914 files (+1 heads) updating to branch default 4019 files updated, 0 files merged, 0 files removed, 0 files unresolved $ cd galaxy-central $ hg branch default $ hg branches default 8885:9852dd712f5c stable 8880:8da37d3985ab $ hg checkout stable abort: path 'static/june_2007_style/Makefile' traverses symbolic link 'static/june_2007_style' I was actually trying to checkout one of my own branches, having setup the .hg/hgrc to include a link to my own fork on bitbucket. Thanks! Peter

4 10

Speed up the galaxy
by 泽蔡 25 Apr '13

25 Apr '13

Hi all, How can I speed up the galaxy? Like how to use more cores and memeries.

6 15

Puzzling test failure with data_column parameter
by Peter Cock 24 Apr '13

24 Apr '13

Hi all, I'm working on a FASTA filter script, as per this email: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003819.html Current code here: http://bitbucket.org/peterjc/galaxy-central/src/c3ac6d7a02f7/ I've added a basic test, but it won't run (see output below). I think the interesting bit of the error output is this exception: cannot find value/label "blastp_four_human_vs_rhodopsin.tabular" in list control, coming from function set_form_control_value in the twill.utils module. This is something to do with the columns parameter, a multiselect option referencing the columns in this tabular file. Removing the validator makes no difference. However, if I change the columns parameter to a plain text parameter, the test passes: $ hg diff diff -r c3ac6d7a02f7 tools/fasta_tools/fasta_filter_by_id.xml --- a/tools/fasta_tools/fasta_filter_by_id.xml Tue Nov 23 11:37:35 2010 +0000 +++ b/tools/fasta_tools/fasta_filter_by_id.xml Tue Nov 23 14:03:31 2010 +0000 @@ -4,9 +4,7 @@ <inputs> <param name="input_fasta" type="data" format="fasta" label="FASTA file to filter on the identifiers"/> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTA identifiers"/> - <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing FASTA identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> - <validator type="no_options" message="Pick at least one column"/> - </param> + <param name="columns" type="text" label="Column(s) containing FASTA identifiers" /> </inputs> <outputs> <data name="output_pos" format="fasta" label="With matched ID" /> I've tried searching the provided wrappers for similar examples (column multi-select from a tabular file). I found filters/uniq.xml (works but uses a bed file rather than a simple tabular file) and stats/cor.xml (needs R and rpy which I don't have installed yet) which have tests, and finally plotting/bar_chart.xml which has no unit tests. Would someone familiar with the internals of the Galaxy tests and how they set tool parameters be able to try reproducing this for me? The branch has all the unit test files required, and there are no new dependencies needed. Thank you, Peter -- Here is the output (on Linux - other tests tried pass): $ ./run_functional_tests.sh -id fasta_filter_by_id ... nose.plugins.manager DEBUG 2010-11-23 13:59:32,958 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy nose.plugins.manager DEBUG 2010-11-23 13:59:32,961 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTestDiff nose.plugins.manager DEBUG 2010-11-23 13:59:32,962 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML Filter sequences by ID ( fasta_filter_by_id ) > Test-1 ... galaxy.tools.actions.upload_common INFO 2010-11-23 13:59:34,905 tool upload1 created job id 1 galaxy.jobs DEBUG 2010-11-23 13:59:42,709 dispatching job 1 to local runner galaxy.jobs INFO 2010-11-23 13:59:42,899 job 1 dispatched galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:43,213 executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:44,033 execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs DEBUG 2010-11-23 13:59:44,414 job 1 ended galaxy.tools.actions.upload_common INFO 2010-11-23 13:59:49,927 tool upload1 created job id 2 galaxy.jobs DEBUG 2010-11-23 13:59:50,067 dispatching job 2 to local runner galaxy.jobs INFO 2010-11-23 13:59:50,702 job 2 dispatched galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:52,059 executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs.runners.local DEBUG 2010-11-23 13:59:52,874 execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs DEBUG 2010-11-23 13:59:53,420 job 2 ended base.twilltestcase DEBUG 2010-11-23 13:59:53,747 In submit_form, continuing, but caught exception: cannot find value/label "blastp_four_human_vs_rhodopsin.tabular" in list control base.twilltestcase DEBUG 2010-11-23 13:59:54,488 ## files diff on /home/pjcock/repositories/galaxy-central/test-data/four_human_proteins_filter_a.fasta and /tmp/tmpijWxYGfour_human_proteins_filter_a.fasta lines_diff=0, found diff = 61 FAIL ====================================================================== FAIL: Filter sequences by ID ( fasta_filter_by_id ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py", line 160, in test_tool self.do_it( td ) File "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py", line 101, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes ) File "/home/pjcock/repositories/galaxy-central/test/base/twilltestcase.py", line 656, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 1 different than expected, difference (using diff): --- local_file +++ history_data @@ -1,2 +1,61 @@ +>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 +MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF +SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK +REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER +VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD +CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF +HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL +>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 +MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG +GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS +DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD +LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP +DPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDT +IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE +ILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ +QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQY +QQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV +ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSD +KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPE +NLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA +QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK +APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARR +HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS +WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ +SQQSQPVELDPFGAAPFPSKQ +>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 +MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL +QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL +VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE +ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG +CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC +TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL -------------------- >> begin captured stdout << --------------------- Uploaded file: four_human_proteins.fasta , ftype: fasta , extra: {'ftype': 'fasta', 'value': 'four_human_proteins.fasta', 'children': []} Uploaded file: blastp_four_human_vs_rhodopsin.tabular , ftype: tabular , extra: {'ftype': 'tabular', 'value': 'blastp_four_human_vs_rhodopsin.tabular', 'children': []} form 'tool_form' contains the following controls ( note the values ) control 0: <HiddenControl(tool_id=fasta_filter_by_id) (readonly)> control 1: <HiddenControl(tool_state=800255c1626362313139396662383639346664316133316565303361646336323163663764636566333538623a376232323566356637303631363736353566356632323361323033303263323032323639366537303735373435663636363137333734363132323361323032323331323232633230323236333666366337353664366537333232336132303232366537353663366332323263323032323639366537303735373435663734363136323735366336313732323233613230323233323232376471002e) (readonly)> control 2: <SelectControl(input_fasta=[*1])> control 3: <SelectControl(input_tabular=[*2])> control 4: <SelectControl(columns=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12])> control 5: <SubmitControl(runtool_btn=Execute) (readonly)> page_inputs (0) {'input_fasta': ['four_human_proteins.fasta'], 'columns': ['1'], 'input_tabular': ['blastp_four_human_vs_rhodopsin.tabular']} --------------------- >> end captured stdout << ---------------------- -------------------- >> begin captured logging << -------------------- galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.jobs: DEBUG: dispatching job 1 to local runner galaxy.jobs: INFO: job 1 dispatched galaxy.jobs.runners.local: DEBUG: executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs.runners.local: DEBUG: execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmpOVlriT 1:/home/pjcock/repositories/galaxy-central/database/job_working_directory/1/dataset_1_files:/tmp/tmpu4uu_o/database/files/000/dataset_1.dat galaxy.jobs: DEBUG: job 1 ended galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2 galaxy.jobs: DEBUG: dispatching job 2 to local runner galaxy.jobs: INFO: job 2 dispatched galaxy.jobs.runners.local: DEBUG: executing: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs.runners.local: DEBUG: execution finished: python /home/pjcock/repositories/galaxy-central/tools/data_source/upload.py /home/pjcock/repositories/galaxy-central /home/pjcock/repositories/galaxy-central/datatypes_conf.xml /tmp/tmp6Z76yl 2:/home/pjcock/repositories/galaxy-central/database/job_working_directory/2/dataset_2_files:/tmp/tmpu4uu_o/database/files/000/dataset_2.dat galaxy.jobs: DEBUG: job 2 ended base.twilltestcase: DEBUG: In submit_form, continuing, but caught exception: cannot find value/label "blastp_four_human_vs_rhodopsin.tabular" in list control base.twilltestcase: DEBUG: ## files diff on /home/pjcock/repositories/galaxy-central/test-data/four_human_proteins_filter_a.fasta and /tmp/tmpijWxYGfour_human_proteins_filter_a.fasta lines_diff=0, found diff = 61 --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 1 test in 21.504s FAILED (failures=1) functional_tests.py INFO 2010-11-23 13:59:54,494 Shutting down functional_tests.py INFO 2010-11-23 13:59:54,494 Shutting down embedded web server functional_tests.py INFO 2010-11-23 13:59:54,497 Embedded web server stopped functional_tests.py INFO 2010-11-23 13:59:54,497 Shutting down app galaxy.jobs INFO 2010-11-23 13:59:54,497 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:54,498 job queue stopped galaxy.jobs.runners.local INFO 2010-11-23 13:59:54,498 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2010-11-23 13:59:54,498 local job runner stopped galaxy.jobs INFO 2010-11-23 13:59:54,499 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:54,499 job stopper stopped functional_tests.py INFO 2010-11-23 13:59:54,499 Embedded Universe application stopped functional_tests.py INFO 2010-11-23 13:59:54,500 Cleaning up temporary files in /tmp/tmpu4uu_o galaxy.jobs INFO 2010-11-23 13:59:55,410 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:55,411 job queue stopped galaxy.jobs.runners.local INFO 2010-11-23 13:59:55,411 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2010-11-23 13:59:55,411 local job runner stopped galaxy.jobs INFO 2010-11-23 13:59:55,411 sending stop signal to worker thread galaxy.jobs INFO 2010-11-23 13:59:55,412 job stopper stopped 'run_functional_tests.sh help' for help Note: galaxy test framework uses tool_conf.xml.sample, not tool_conf.xml

2 3

resubmit a job if the node fails
by zhengqiu cai 10 Apr '13

10 Apr '13

Hi, Can Galaxy resubmit a job if the node where the job is running fails? I know sge can do that by using qsub -r. It should be very useful if Galaxy can do that. Thank you, Cai

3 2

How to test DRMAA configuration?
by Joshua Orvis 09 Apr '13

09 Apr '13

I have a working local Galaxy instance and wanted to enable DRMAA support to utilize our SGE (or LSF) grid. Following the guide here<http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster> I set what I appeared to need to make this work. From the DRMAA_LIBRARY_PATH env variable to all the configuration settings in universe_wsgi.ini, reconfiguring the server hosting Galaxy as a submit host, etc. Some specific config file changes made: new_file_path = /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/tmp start_job_runners = drmaa default_cluster_job_runner = drmaa:/// set_metadata_externally = True outputs_to_working_directory = True I then killed and restarted the Galaxy instance and tried a simple FASTQ -> FASTA test execution, but it ran locally. I couldn't find any sort of errors or messages related to DRMAA in the server log, and the job ran to completion. I commented out the local tool runner overrides. What can I do to test my DRMAA configuration and where should I look for errors? Thanks - Joshua

3 4

Problems with rsync from datacache.g2.bx.psu.edu/indexes
by Rodolfo Aramayo 20 Mar '13

20 Mar '13

Hi, I hope this is the right place to ask, I am trying to rsync from: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ and I am getting the error: @ERROR: chroot failed rsync error: error starting client-server protocol (code 5) at main.c(1534) [Receiver=3.0.9 I know I can rsync to any other places Do you happen to know what is going on? Thanks --Rodolfo

3 2

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

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galaxy-dev February 2013