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

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

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Output a file stored within a server directory to the current history in galaxy
by Venice Margarette Juanillas 24 Apr '13

24 Apr '13

Hi all, I'm Venice and I'm working on a local galaxy instance here at IRRI. This question might sound really naive but I really can't work around it. I'm creating an xml for a tool where the user will select a list of file names from the drop-down as input. I stored these files in a directory within galaxy-dist. Based on the user input, Galaxy must output the user-selected file. I created this xml: <tool id="matrix2flapjack" name="NT Matrix to Flapjack"> <description>file conversion</description> <command interpreter="perl">matrix2flapjack.pl $inputFile $outputFile $snp_map</command> <inputs> <param format="tabular" name="inputFile" type="data" label="Nucleotide Matrix file"/> <param name="snp_map" type="select" label="SNP map file"> <option value="/home/galaxy/galaxy-dist/SNP_maps/11861_snp_map.txt">11861</option> <option value="/home/galaxy/galaxy-dist/SNP_maps/11862_snp_map.txt">11862</option> <option value="/home/galaxy/galaxy-dist/SNP_maps/13033_snp_map.txt">13033</option> </param> </inputs> <outputs> <data format="tabular" name="outputFile" label="Flapjack Format of ${inputFile.name} "> </data> <data format="tabular" name="snp_map" label="SNP Map"/> </outputs> <help> This tool converts a SNP NT matrix file to Flapjack file format. </help> </tool> However, it doesn't output the file. Instead, it prompts, "Either the dataset does not exist or you don't have permission to access it." Thanks in advance for your reply. Thanks and Best regards, Venice

1 0

Run Jobs as Real User - Unable to get working with Drmaa (SGE) and job_conf.xml
by Adam Brenner 23 Apr '13

23 Apr '13

I have the following job_conf.xml file setup for our cluster: http://pastebin.com/raw.php?i=0uNhcVJk When running jobs from my admin account via Galaxy it runs under the same user as galaxy is, for testing, this as root. I need for it to run under the real user. The email address / galaxy account I am using to test with does match with a user on the cluster -- user(a)example.com where user is a valid user account with correct permissions to run jobs on our cluster and queue. I followed the information here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_J… Any ideas as to why galaxy_external* is not being called? The paster.log file does not show anything useful regarding calling external scripts. -- 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/ aebrenne(a)uci.edu

1 2

Problem using FTP upload
by Jillian Rowe 23 Apr '13

23 Apr '13

Hello, I would like to use the FTP upload option without actually having an FTP service setup. Instead users will scp to the directory. ftp_upload_dir = import/users ftp_upload_site = notnothing if a create a import/users/username with username as my login I still get the message: Your FTP upload directory contains no files. This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password). According to this email tot he mailing list http://gmod.827538.n3.nabble.com/Configuring-Galaxy-for-FTP-upload-td393419… I thought I could do a setup such as I am trying now, but now I am not so sure. Any ideas? Best, Jillian

2 5

ToolShed test complaining core bundled test file is missing
by Peter Cock 23 Apr '13

23 Apr '13

Hi Greg/Dave, I've noticed an oddity with another unit test failure on the main Tool Shed, http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss Revision: 1:922d69bd5258 Tool id: get_orfs_or_cdss version: 0.0.2 Reason test is invalid One or more test files are missing for tool get_orfs_or_cdss: Ssuis.fasta The tool tests should be failing as they are omitting some test files, which I'd not included in the uploaded tar ball (I'll fix this shortly): test-data/get_orf_input.fasta test-data/get_orf_input.Suis_ORF.nuc.fasta test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.t11_nuc_out.fasta test-data/get_orf_input.t11_open_nuc_out.fasta test-data/get_orf_input.t11_open_prot_out.fasta test-data/get_orf_input.t11_prot_out.fasta test-data/get_orf_input.t1_nuc_out.fasta test-data/get_orf_input.t1_prot_out.fasta However, I believe the ToolShed warning is misleading as test-data/Ssuis.fasta is already present as part of the Galaxy core install. This is why I have used it (and other bundled files like it) to minimise the download size of the tool itself. Thanks, Peter

2 2

ToolShed test failure, "blastxml" ItemNotFoundError
by Peter Cock 23 Apr '13

23 Apr '13

Hi all, I'm seeing a unit test failure on the Tool Shed which I think is in some way related to the blast_datatypes dependency not refreshing the list of available file formats: http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr Revision: 7:a7add03a44fd - blastxml_to_top_descr v0.0.6 Tool shed version: 9471:ae53deed05b6 Galaxy version: 9505:1e3d92ec22b2 Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 43, in do_it shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 193, in upload_file self.refresh_form( "file_type", ftype ) #Refresh, to support composite files File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in refresh_form tc.fv( f.name, control.name, value ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/commands.py", line 450, in formvalue set_form_control_value(control, value) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/utils.py", line 190, in set_form_control_value raise ClientForm.ItemNotFoundError('cannot find value/label "%s" in list control' % (val,)) ItemNotFoundError: cannot find value/label "blastxml" in list control This bug reminds me of something recently discussed on the list, but I can't find the thread (perhaps it was another file format). So there may already be a Trello issue open for this. Thanks, Peter

2 2

Automatics Tool Shed tests - failed dependency installation?
by Peter Cock 22 Apr '13

22 Apr '13

Hi all, Over on the test Tool Shed, I'm trying to include automated installation of NLStradamus as part of my wrapper for this NLS prediction tool. This should make things simper for end users, but is also intended to get the unit tests to pass on the Galaxy Tool Shed setup. The repo is here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus The unit tests are still failing, just saying: Fatal error: Exit code 127 () /bin/sh: 1: NLStradamus: not found The tool XML file contains an explicit package dependency: <requirements> <requirement type="binary">NLStradamus</requirement> <requirement type="package" version="1.8">NLStradamus</requirement> </requirements> That package dependency is defined using the tool_dependencies.xml file (in the same repository). My tool_dependencies.xml file should compile this binary, and have it added to the $PATH. This error message suggests that this did not work: <?xml version="1.0"?> <tool_dependency> <package name="NLStradamus" version="1.8"> <install version="0.0.1"> <actions> <action type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8…</action>  <action type="shell_command">g++ NLStradamus.cpp -o NLStradamus -O3</action> <action type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> ... My question is was my tool_dependencies.xml file processed, and if so did it run without errors, and if so why didn't it work? If there were errors processing the tool_dependencies.xml then I would hope the ToolShed would show them (and not silently overlook this and attempt to run the tests anyway). Is that the case? Thanks, Peter

3 5

Problem uploading file !!
by Nishant THAKUR 22 Apr '13

22 Apr '13

Hello, I installed galaxy server on ubuntu recently, I can upload small fastq files (~600 Mb), but when I am uploading large file(2.7 gb), it is taking forever. Could you please suggest me something ? Best regards Nishant Thakur

3 2

download URLs limited to twelve?
by Shantanu Pavgi (Campus) 21 Apr '13

21 Apr '13

One of our users is trying to download thousands of files by pasting their URLs in 'URL/Text' box of the upload tool. It seems like Galaxy selects only first 12 URLs and ignores rest of them. The issue can be reproduced on the main public Galaxy<https://main.g2.bx.psu.edu/> instance as well. I was wondering how can we remove this limit so that users can queue up thousands of download jobs in one click. Any help? -- Thanks, Shantanu

1 0

directory copies as zero-length file from job_working_directory?
by Nikhil Joshi 20 Apr '13

20 Apr '13

Hi all, So I have a tool that I am writing a wrapper script for that produces a directory of images as one of its outputs. This directory gets created just fine in the job_working_directory, but then when the job finishes and the contents of the job_working_directory are copied, the copy of the images directory is a zero-length *file*. I seem to recall having this problem before and finding a solution to it, but now I can't seem to find it. Any ideas? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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