Great! Thanks! Don't you ever sleep? It must be some un-allah-ly hour where you are.
On Thu, Sep 26, 2013 at 8:55 PM, Greg Von Kuster <g...@bx.psu.edu> wrote: > 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 > 31:5b6af671d985 28:c4ee2e69d691 3:fe5c828dee80 *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<http://testtoolshed.g2.bx.psu.edu/repository/browse_repository?id=347ec9acdc3b02e8> > 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<http://testtoolshed.g2.bx.psu.edu/repository/view_changelog?id=347ec9acdc3b02e8> > Owner:fubar > Times downloaded:15 > Dependencies of this repository > > Repository dependencies* - installation of these additional repositories > is > required*<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&message=&id=347ec9acdc3b02e8> > > Tool dependencies* - repository tools require handling of these > dependencies*<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&message=&id=347ec9acdc3b02e8> > > Contents of this repository > > Valid tools* - click the name to preview the tool and use the pop-up menu > to inspect all > metadata*<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&message=&id=347ec9acdc3b02e8> > > Automated tool test results > > Tool test > results<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&message=&id=347ec9acdc3b02e8> > Automated test > environment<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&message=&id=347ec9acdc3b02e8> > Tests that > failed<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&message=&id=347ec9acdc3b02e8> > *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 1.40214375755809e-09 17.2776088871455 6164 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a> > -Mir208b -12.4332279840446 4.60762179736006 -19.5924575126382 > 1.17919871718875e-11 2.69093147262473e-09 15.6836663826186 14756 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir208b' > >Mir208b</a> > -Mir10b -5.1309149063532 12.2628671946242 -18.2420234752943 > 3.12499057505143e-11 4.96397841614262e-09 16.2215027882858 197340 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a> > -Mir143hg -2.24922058313374 16.2444825488726 -18.0824813146443 > 3.52173903971276e-11 4.96397841614262e-09 16.0266951625541 1407364 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg' > >Mir143hg</a> > -Mir143 -2.25106712131643 16.235859869169 -18.0814805993441 > 3.524391092512e-11 4.96397841614262e-09 16.0260836456534 1399819 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a> > -Mir499 -11.5675289490546 3.78745976580796 -17.9420857279689 > 3.91549568319751e-11 4.96397841614262e-09 14.8217405828874 6527 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a> > -Mir802 9.15843445824816 2.91576747878654 17.3165224121399 > 6.33861560587965e-11 7.23236040630868e-09 14.381577240531 1514 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a> > -Mir3073 8.42054159318439 2.54571889776166 16.7026571721381 > 1.03306635740721e-10 1.03604453339228e-08 13.9858447292853 904 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir3073' > >Mir3073</a> > -Mir148a 2.63821345578617 15.4435819751152 16.5481882215215 > 1.17118649515038e-10 1.03604453339228e-08 14.8147917664862 1002397 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir148a' > >Mir148a</a> > -Mir101b 3.76572195114225 10.8508440499081 16.5385659719288 > 1.1804188373444e-10 1.03604453339228e-08 14.9000274171241 59019 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir101b' > >Mir101b</a> > -Mir490 -8.47437764634465 3.75069567634692 -16.2596504905533 > 1.48481644820999e-10 1.21012540529114e-08 13.4246171016517 1741 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a> > -Mir21 2.93853744034991 13.1642916950886 15.3754036511693 > 3.14833456057776e-10 2.39483315574615e-08 13.8676979022068 229120 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a> > -Mir181c -3.74256009957124 9.62955774646065 -15.2423608550805 > 3.53706264458683e-10 2.52236779842098e-08 13.8104046176901 23605 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir181c' > >Mir181c</a> > -Mir204 -7.68442507149438 4.77517348536933 -15.0334839919296 > 4.2542677795722e-10 2.85536443323052e-08 12.8224274879526 2601 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a> > -Mir23a -3.16576837850821 8.78965917558611 -14.6311785109623 > 6.11068192724496e-10 3.87349337721472e-08 13.2691736804205 10118 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a> > -Mir181d -3.63621106402109 6.37132182424908 -14.3170733565449 > 8.15750840848868e-10 4.89879847057136e-08 12.9563328312209 2139 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir181d' > >Mir181d</a> > -Mir133b -6.49354876170712 1.25448620431148 -13.969968060601 > 1.12993427319653e-09 6.44627502858619e-08 11.9826837063041 159 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir133b' > >Mir133b</a> > -Mir27a -3.10693537246128 9.92557960348829 -13.8382510839158 > 1.28101104196848e-09 6.96015999469543e-08 12.5130856443239 21886 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a> > -Mir194-2 5.26413595786074 6.08976151689046 13.0440120203829 > 2.79288399641768e-09 1.44849119996026e-07 11.7157527118771 3570 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2' > >Mir194-2</a> > -Mir195 -3.21659545049586 7.4509349905835 -12.869478368273 > 3.33278798407795e-09 1.65335264775345e-07 11.5875227405737 3962 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a> > -Mir27b -1.97637614533106 15.0957731023791 -11.75603589654 > 1.08219717999805e-08 5.14494575990741e-07 10.1277185662145 625308 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a> > -Mir378 -3.09739319841142 7.38320489393809 -11.6841625470748 > 1.17137125863851e-08 5.34613842442616e-07 10.3296922348831 4075 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a> > -Snord104 2.33737428989677 10.6109023861403 11.4956750870273 > 1.44448164322638e-08 6.33905213431269e-07 10.0233949189609 33458 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Snord104' > >Snord104</a> > -Mir1983 -5.89550024150745 0.993185099223749 -11.4458119994178 > 1.52754786535047e-08 6.44160462853232e-07 9.74926029381244 101 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir1983' > >Mir1983</a> > -Mir322 -3.29661750880005 8.21534154356388 -11.4153616003567 > 1.58076187203247e-08 6.44160462853232e-07 10.0084716002011 7074 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a> > -Mir200a 6.19156065085543 1.79813092499896 11.3221723123067 > 1.75622912046568e-08 6.9098531946598e-07 9.66229453831667 264 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir200a' > >Mir200a</a> > -Mir215 -3.04587333807051 5.75442336214621 -11.1481336257529 > 2.14182153707674e-08 8.08245865886245e-07 9.75326755116029 1182 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a> > -Dnm3os -3.36334357719079 5.86074322417943 -11.0922610835813 > 2.28395969947309e-08 8.08245865886245e-07 9.68949616901383 1401 <a href=' > http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a> > -Mir182 4.90399541739044 7.1511683493624 11.0744681203078 > 2.33130367310143e-08 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.laza...@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.laza...@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.c...@googlemail.com>wrote: > >> On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <d...@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/09a68a90d552 >> - 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/ >> >> 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/ > > > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
___________________________________________________________ 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/
