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(a)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/repos...
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/...
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...
Tool dependencies* - repository tools require handling of these
dependencies*<http://testtoolshed.g2.bx.psu.edu/repository/view_reposi...
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...
Automated tool test results
Tool test
results<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?s...
Automated test
environment<http://testtoolshed.g2.bx.psu.edu/repository/view_reposito...
Tests that
failed<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?st...
*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/differentia...
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
Statistics
On Sep 26, 2013, at 6:47 AM, Ross <ross.lazarus(a)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(a)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(a)googlemail.com>wrote:
> On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <dave(a)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/09a68a90...
> - 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:
>
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>
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>
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>
___________________________________________________________
Please keep all replies on the list by using "reply all"
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To search Galaxy mailing lists use the unified search at:
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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444