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 <greg@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
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Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository 'differential_count_models'
Unrestricted
edgeR, DESeq2 and voom in one tool
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.
fubar
15


Automated tool test results

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 @@
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Categories
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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:

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/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
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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ