There seems to be issues with some repositories which we'll need to track down. However, I fixed some issues yesterday with styles in the tool shed that kep the tool tests from displaing, and now test results are displaying at least for this repository: Repository revision repository tip Select a revision to inspect and download versions of Galaxy utilities from this repository. Repository 'differential_count_models' Sharable link to this repository: http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models Clone this repository: hg clone http://testtoolshed.g2.bx.psu.edu/repos/fubar/differential_count_models Name: differential_count_models Repository type: Unrestricted Synopsis: edgeR, DESeq2 and voom in one tool Detailed description: edgeR, DESeq2 and voom for replicate RNA seq data. 1) TURN OFF HTML SANITIZATION in universe_wsgi.xml or your outputs will lack proper style sheets and look awful 2) This packages dependencies include R and bioconductor so expect your proxy to time out during the installation - be patient - it takes 10 to 30 minutes to download and compile everything, depending on the velocity of your machine and the interwebs - about 20 minutes on my laptop. 3) make sure you have a $TMP set in your environment or ghostscript gets unhappy - you'll see a warning every time you run this tool if you've forgotten. Revision: 31:5b6af671d985 Owner: fubar Times downloaded: 15 Dependencies of this repository Repository dependencies - installation of these additional repositories is required Tool dependencies - repository tools require handling of these dependencies Contents of this repository Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata Automated tool test results Tool test results Automated test environment Tests that failed Tool id: rgDifferentialCount Tool version: rgDifferentialCount Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/fubar/differential_count_models/rgDifferentialCount/0.21) Stderr: Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-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-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsubztFQ/testtoolshed.g2.bx.psu.edu/repos/fubar/differential_count_models/5b6af671d985/differential_count_models/differential_count_models/test-data/edgeRtest1out.xls v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpFGK1x1/tmpCzIKTPedgeRtest1out.xls ) --- local_file +++ history_data @@ -1,1142 +0,0 @@ -ID logFC AveExpr t P.Value adj.P.Val B NReads URL -Mir192 6.94888256843679 14.6763802609023 42.7229535356942 2.30119906424271e-16 2.62566813230094e-13 27.2664713266936 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a> -Mir208a -11.0150177152075 3.93955375669227 -23.2524066836307 1.11893807599952e-12 6.38354172357727e-10 17.2086622097974 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a> -Mir122a 10.4261254701779 8.16986409392255 21.7229119192922 2.85968233611017e-12 1.08763251516723e-09 17.760171141852 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a> -Mir149 -7.03046258655617 6.31608073609863 -20.8838348040628 4.91549082404237e-12 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8.08245865886245e-07 9.65884218207857 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a> -Mir181a-2 -3.04829832099813 6.94146510070354 -11.0721276255975 2.33760855164295e-08 8.08245865886245e-07 9.64401697815694 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a> -Mir1948 7.19552540631629 4.5513492833967 11.0054920626234 2.52493600829575e-08 8.47338819254543e-07 9.34179361673467 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a> -Mir214 -3.28087400431203 5.47844506177362 -10.7682572190636 3.3325545851092e-08 1.0864127947456e-06 9.3185039394887 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a> -Mir153 -5.9638030672045 1.43863148956561 -10.7270821099311 3.49874201497232e-08 1.09398957489501e-06 9.03556928822473 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a> Categories Statistics On Sep 26, 2013, at 6:47 AM, Ross <ross.lazarus@gmail.com> wrote:
+1
I think it's been a problem with some of my repos for a while on test so possible not related to blast_datatypes - I sent this privately about 2 weeks ago:
Ross <ross.lazarus@gmail.com> Sep 13 (13 days ago)
to Dave, Greg
Hey Dave - any thoughts on how to fix http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models so the test results appear? AFAIK the test works but there's no test results section in the manage repository sections I can see.
On Thu, Sep 26, 2013 at 8:40 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote: On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
The one on the main tool shed is due to an issue Greg and I are in the process of resolving. As soon as we've tested the fix, I'll schedule a re-test of that repository and update you on the status.
--Dave B.
Looks to be spreading, or linked to the blast_datatypes dependency? Listed under "Latest revision: failing tool tests"
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93 - missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d55... - missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680 - failed as expected (missing Biopython dependency, see separate thread about the ALTAS dependency problem)
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d - failing as expected (missing R dependency)
And over on the Test Tool Shed (which was offline but recently came back up), listed under "Latest revision: failing tool tests":
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d - missing test results
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e - missing test results
Regards,
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/
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