test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

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test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

Peter Cock
Hi all,

I have a query about a failing tool test on the Tool Shed, where it
seems Galaxy is trying to convert both the expected BAM output
and the tool's BAM output into SAM for comparison - but this
fails.

https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

2015-01-27 02:13:51
...
Tool id: samtools_depad
Tool version: samtools_depad
Test: test_tool_000000
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
Stderr:
Traceback:
Traceback (most recent call last):
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 122, in test_tool
    self.do_it( td )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 40, in do_it
    self._verify_outputs( testdef, test_history, jobs, shed_tool_id,
data_list, galaxy_interactor )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 80, in _verify_outputs
    galaxy_interactor.verify_output( history, jobs, output_data,
output_testdef=output_testdef, shed_tool_id=shed_tool_id,
maxseconds=maxseconds )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py",
line 66, in verify_output
    self.twill_test_case.verify_hid( outfile, hda_id=hid,
attributes=attributes, dataset_fetcher=fetcher,
shed_tool_id=shed_tool_id )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 2341, in verify_hid
    raise AssertionError( errmsg )
AssertionError: History item  different than expected, difference (using diff):
( /tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam
v. /tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpExQWRD/tmpSknKqLsam_spec_padded.depad.bam
)
Converting local (test-data) bam to sam failed

(and same error on the second test)

The same occurs on the Test Tool Shed (with a very slightly updated
version of this tool), although with a more concise traceback:

https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

2015-01-25 08:21:59
...
Tool id: samtools_depad
Tool version: samtools_depad
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
Stderr:
Traceback:
Traceback (most recent call last):
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 268, in test_tool
    self.do_it( td )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 67, in do_it
    raise e
JobOutputsError: History item  different than expected, difference (using diff):
( /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam
v. /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam
)
Converting local (test-data) bam to sam failed

Both tests should produce a BAM file matching the provided
test-data/sam_spec_padded.depad.bam example. The error
comes from test/base/twilltestcase.py,

        p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % (
temp_local.name, local_name  ), shell=True )
        assert not p.wait(), 'Converting local (test-data) bam to sam failed'

Running this command locally at the terminal seems to work fine,
both with samtools 0.1.19 and 1.1.

$ ~/bin/samtools_0.1.19 view -h -o temp.sam sam_spec_padded.depad.bam
$ more temp.sam
@HD    VN:1.5    SO:coordinate
@SQ    SN:ref    LN:45
ref    516    ref    1    0    45M    *    0    0
AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT    *
r001    99    ref    7    30    8M2I4M1D3M    =    37    41
TTAGATAAAGGATACTG    *
*    768    ref    8    30    1M    *    0    0    *    *
CT:Z:.;Warning;Note=Ref wrong?
r002    0    ref    9    30    3S6M1P1I4M    *    0    0
AAAAGATAAGGATA    *    PT:Z:1;4;+;homopolymer
r003    0    ref    9    30    5H6M    *    0    0    AGCTAA    *    NM:i:1
r004    0    ref    16    30    6M14D5M    *    0    0    ATAGCTTCAGC    *
r003    2064    ref    29    30    6H5M    *    0    0    TAGGC    *    NM:i:0
r001    147    ref    37    30    9M    =    7    -41    CAGCGGCAT
*    NM:i:1

$ ~/bin/samtools_1.1 view -h -o temp.sam sam_spec_padded.depad.bam
[galaxy@ppserver test-data]$ more temp.sam
@HD    VN:1.5    SO:coordinate
@SQ    SN:ref    LN:45
ref    516    ref    1    0    45M    *    0    0
AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT    *
r001    99    ref    7    30    8M2I4M1D3M    =    37    41
TTAGATAAAGGATACTG    *
*    768    ref    8    30    1M    *    0    0    *    *
CT:Z:.;Warning;Note=Ref wrong?
r002    0    ref    9    30    3S6M1P1I4M    *    0    0
AAAAGATAAGGATA    *    PT:Z:1;4;+;homopolymer
r003    0    ref    9    30    5H6M    *    0    0    AGCTAA    *    NM:i:1
r004    0    ref    16    30    6M14D5M    *    0    0    ATAGCTTCAGC    *
r003    2064    ref    29    30    6H5M    *    0    0    TAGGC    *    NM:i:0
r001    147    ref    37    30    9M    =    7    -41    CAGCGGCAT
*    NM:i:1


Which version of samtools is on the $PATH on the test system?

Could the test system have run out of disk space again?

The tests are passing on my local development instance (before
and after updating to latest galaxy-central), and on TravisCI using
the latest Galaxy: https://travis-ci.org/peterjc/pico_galaxy/builds/48485673

Thanks,

Peter
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Re: test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

Peter Cock
On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <[hidden email]> wrote:

> Hi all,
>
> I have a query about a failing tool test on the Tool Shed, where it
> seems Galaxy is trying to convert both the expected BAM output
> and the tool's BAM output into SAM for comparison - but this
> fails.
>
> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>
> 2015-01-27 02:13:51
> ...
> Tool id: samtools_depad
> Tool version: samtools_depad
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
> Stderr:
> Traceback:
> Traceback (most recent call last):
>   File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 122, in test_tool
>     self.do_it( td )
>   File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 40, in do_it
>     self._verify_outputs( testdef, test_history, jobs, shed_tool_id,
> data_list, galaxy_interactor )
>   File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 80, in _verify_outputs
>     galaxy_interactor.verify_output( history, jobs, output_data,
> output_testdef=output_testdef, shed_tool_id=shed_tool_id,
> maxseconds=maxseconds )
>   File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py",
> line 66, in verify_output
>     self.twill_test_case.verify_hid( outfile, hda_id=hid,
> attributes=attributes, dataset_fetcher=fetcher,
> shed_tool_id=shed_tool_id )
>   File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
> line 2341, in verify_hid
>     raise AssertionError( errmsg )
> AssertionError: History item  different than expected, difference (using diff):
> ( /tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam
> v. /tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpExQWRD/tmpSknKqLsam_spec_padded.depad.bam
> )
> Converting local (test-data) bam to sam failed
>
> (and same error on the second test)

https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing,
although now with a more concise traceback:

Test runs
2015-01-29 02:26:31
Automated test environment
Tests that failed
Tool id: samtools_depad
Tool version: samtools_depad
Test: test_tool_000000
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
Stderr:
Traceback:
Traceback (most recent call last):
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 122, in test_tool
    self.do_it( td )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 40, in do_it
    self._verify_outputs( testdef, test_history, jobs, shed_tool_id,
data_list, galaxy_interactor )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 80, in _verify_outputs
    galaxy_interactor.verify_output( history, jobs, output_data,
output_testdef=output_testdef, shed_tool_id=shed_tool_id,
maxseconds=maxseconds )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py",
line 66, in verify_output
    self.twill_test_case.verify_hid( outfile, hda_id=hid,
attributes=attributes, dataset_fetcher=fetcher,
shed_tool_id=shed_tool_id )
  File "/tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 2341, in verify_hid
    raise AssertionError( errmsg )
AssertionError: History item  different than expected, difference (using diff):
( /tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/2d303f2e09e0/samtools_depad/test-data/sam_spec_padded.depad.bam
v. /tmp/buildslave/buildbot-install-test-main-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpfD5MDC/tmpOpbQxNsam_spec_padded.depad.bam
)
Converting local (test-data) bam to sam failed



> The same occurs on the Test Tool Shed (with a very slightly updated
> version of this tool), although with a more concise traceback:
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>
> 2015-01-25 08:21:59
> ...
> Tool id: samtools_depad
> Tool version: samtools_depad
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
> Stderr:
> Traceback:
> Traceback (most recent call last):
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 268, in test_tool
>     self.do_it( td )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 67, in do_it
>     raise e
> JobOutputsError: History item  different than expected, difference (using diff):
> ( /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam
> v. /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam
> )
> Converting local (test-data) bam to sam failed
>

https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also
still failing,

Test runs
2015-01-25 08:21:59
Automated test environment
Tests that failed
Tool id: samtools_depad
Tool version: samtools_depad
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
Stderr:
Traceback:
Traceback (most recent call last):
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 268, in test_tool
    self.do_it( td )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 67, in do_it
    raise e
JobOutputsError: History item  different than expected, difference (using diff):
( /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/8e1e3a1ecad7/samtools_depad/test-data/sam_spec_padded.depad.bam
v. /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpNvCGJi/tmphX3A_Fsam_spec_padded.depad.bam
)
Converting local (test-data) bam to sam failed




> Both tests should produce a BAM file matching the provided
> test-data/sam_spec_padded.depad.bam example. The error
> comes from test/base/twilltestcase.py,
>
>         p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % (
> temp_local.name, local_name  ), shell=True )
>         assert not p.wait(), 'Converting local (test-data) bam to sam failed'
>
> Running this command locally at the terminal seems to work fine,
> both with samtools 0.1.19 and 1.1.
>
> $ ~/bin/samtools_0.1.19 view -h -o temp.sam sam_spec_padded.depad.bam
> $ more temp.sam
> @HD    VN:1.5    SO:coordinate
> @SQ    SN:ref    LN:45
> ref    516    ref    1    0    45M    *    0    0
> AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT    *
> r001    99    ref    7    30    8M2I4M1D3M    =    37    41
> TTAGATAAAGGATACTG    *
> *    768    ref    8    30    1M    *    0    0    *    *
> CT:Z:.;Warning;Note=Ref wrong?
> r002    0    ref    9    30    3S6M1P1I4M    *    0    0
> AAAAGATAAGGATA    *    PT:Z:1;4;+;homopolymer
> r003    0    ref    9    30    5H6M    *    0    0    AGCTAA    *    NM:i:1
> r004    0    ref    16    30    6M14D5M    *    0    0    ATAGCTTCAGC    *
> r003    2064    ref    29    30    6H5M    *    0    0    TAGGC    *    NM:i:0
> r001    147    ref    37    30    9M    =    7    -41    CAGCGGCAT
> *    NM:i:1
>
> $ ~/bin/samtools_1.1 view -h -o temp.sam sam_spec_padded.depad.bam
> [galaxy@ppserver test-data]$ more temp.sam
> @HD    VN:1.5    SO:coordinate
> @SQ    SN:ref    LN:45
> ref    516    ref    1    0    45M    *    0    0
> AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT    *
> r001    99    ref    7    30    8M2I4M1D3M    =    37    41
> TTAGATAAAGGATACTG    *
> *    768    ref    8    30    1M    *    0    0    *    *
> CT:Z:.;Warning;Note=Ref wrong?
> r002    0    ref    9    30    3S6M1P1I4M    *    0    0
> AAAAGATAAGGATA    *    PT:Z:1;4;+;homopolymer
> r003    0    ref    9    30    5H6M    *    0    0    AGCTAA    *    NM:i:1
> r004    0    ref    16    30    6M14D5M    *    0    0    ATAGCTTCAGC    *
> r003    2064    ref    29    30    6H5M    *    0    0    TAGGC    *    NM:i:0
> r001    147    ref    37    30    9M    =    7    -41    CAGCGGCAT
> *    NM:i:1
>
>
> Which version of samtools is on the $PATH on the test system?
>
> Could the test system have run out of disk space again?
>
> The tests are passing on my local development instance (before
> and after updating to latest galaxy-central), and on TravisCI using
> the latest Galaxy: https://travis-ci.org/peterjc/pico_galaxy/builds/48485673
>
> Thanks,
>
> Peter

Any ideas? Are any of the other tools on either Tool Shed showing
the same error?

Thanks,

Peter
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Re: test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

Peter Cock
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock <[hidden email]> wrote:

> On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <[hidden email]> wrote:
>> Hi all,
>>
>> I have a query about a failing tool test on the Tool Shed, where it
>> seems Galaxy is trying to convert both the expected BAM output
>> and the tool's BAM output into SAM for comparison - but this
>> fails.
>>
>> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>>
>> 2015-01-27 02:13:51
>> ...
>> Converting local (test-data) bam to sam failed
>>
>> (and same error on the second test)
>
> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing,
> although now with a more concise traceback:
>
> Test runs
> 2015-01-29 02:26:31
> Automated test environment
> Tests that failed
> Tool id: samtools_depad
> Tool version: samtools_depad
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
> Stderr:
> Traceback:
> Traceback (most recent call last):
> ...
> Converting local (test-data) bam to sam failed
>
>> The same occurs on the Test Tool Shed (with a very slightly updated
>> version of this tool), although with a more concise traceback:
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>>
>> 2015-01-25 08:21:59
>> ...
>> Tool id: samtools_depad
>> Tool version: samtools_depad
>> Test: test_tool_000000
>> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
>> Stderr:
>> Traceback:
>> ...
>> Converting local (test-data) bam to sam failed
>>
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also
> still failing,
>
> Test runs
> 2015-01-25 08:21:59
> ...
> Converting local (test-data) bam to sam failed

Still failing on the Test Tool Shed, bug filed on Trello,
https://trello.com/c/TL0IdLlG/2570-toolshed-converting-local-test-data-bam-to-sam-failed

Tests currently stalled on the main Tool Shed, reported here:
http://dev.list.galaxyproject.org/Tests-not-being-run-on-toolsheds-tc4666816.html
https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-March/021708.html

Peter
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Re: test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

John Chilton-4
Hey Peter,

  Thanks for continuing to apply pressure on these issues. I have
pushed some logging into Galaxy's development branch
(https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d)
that should make that error more informative. I don't know when that
will get pushed out to bitbucket and the shed retested - but once
those two things happen we will hopefully have a better idea what the
problem is (probably some subtle deployment problem - some
incompatible version of samtools on the path? samtools on Galaxy's
path but not the test script's path?).

-John


On Mon, Mar 23, 2015 at 6:06 AM, Peter Cock <[hidden email]> wrote:

> On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock <[hidden email]> wrote:
>> On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <[hidden email]> wrote:
>>> Hi all,
>>>
>>> I have a query about a failing tool test on the Tool Shed, where it
>>> seems Galaxy is trying to convert both the expected BAM output
>>> and the tool's BAM output into SAM for comparison - but this
>>> fails.
>>>
>>> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>>>
>>> 2015-01-27 02:13:51
>>> ...
>>> Converting local (test-data) bam to sam failed
>>>
>>> (and same error on the second test)
>>
>> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing,
>> although now with a more concise traceback:
>>
>> Test runs
>> 2015-01-29 02:26:31
>> Automated test environment
>> Tests that failed
>> Tool id: samtools_depad
>> Tool version: samtools_depad
>> Test: test_tool_000000
>> (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
>> Stderr:
>> Traceback:
>> Traceback (most recent call last):
>> ...
>> Converting local (test-data) bam to sam failed
>>
>>> The same occurs on the Test Tool Shed (with a very slightly updated
>>> version of this tool), although with a more concise traceback:
>>>
>>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>>>
>>> 2015-01-25 08:21:59
>>> ...
>>> Tool id: samtools_depad
>>> Tool version: samtools_depad
>>> Test: test_tool_000000
>>> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
>>> Stderr:
>>> Traceback:
>>> ...
>>> Converting local (test-data) bam to sam failed
>>>
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also
>> still failing,
>>
>> Test runs
>> 2015-01-25 08:21:59
>> ...
>> Converting local (test-data) bam to sam failed
>
> Still failing on the Test Tool Shed, bug filed on Trello,
> https://trello.com/c/TL0IdLlG/2570-toolshed-converting-local-test-data-bam-to-sam-failed
>
> Tests currently stalled on the main Tool Shed, reported here:
> http://dev.list.galaxyproject.org/Tests-not-being-run-on-toolsheds-tc4666816.html
> https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-March/021708.html
>
> Peter
> ___________________________________________________________
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Re: test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

Peter Cock
On Mon, Mar 23, 2015 at 1:41 PM, John Chilton <[hidden email]> wrote:

> Hey Peter,
>
>   Thanks for continuing to apply pressure on these issues. I have
> pushed some logging into Galaxy's development branch
> (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d)
> that should make that error more informative. I don't know when that
> will get pushed out to bitbucket and the shed retested - but once
> those two things happen we will hopefully have a better idea what the
> problem is (probably some subtle deployment problem - some
> incompatible version of samtools on the path? samtools on Galaxy's
> path but not the test script's path?).
>
> -John

Lovely - I agree this seems the most likely cause, so fingers crossed.

Thank you,

Peter
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Re: test/base/twilltestcase.py - Converting local (test-data) bam to sam failed

Peter Cock
On Mon, Mar 23, 2015 at 4:00 PM, Peter Cock <[hidden email]> wrote:

> On Mon, Mar 23, 2015 at 1:41 PM, John Chilton <[hidden email]> wrote:
>> Hey Peter,
>>
>>   Thanks for continuing to apply pressure on these issues. I have
>> pushed some logging into Galaxy's development branch
>> (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d)
>> that should make that error more informative. I don't know when that
>> will get pushed out to bitbucket and the shed retested - but once
>> those two things happen we will hopefully have a better idea what the
>> problem is (probably some subtle deployment problem - some
>> incompatible version of samtools on the path? samtools on Galaxy's
>> path but not the test script's path?).
>>
>> -John
>
> Lovely - I agree this seems the most likely cause, so fingers crossed.
>
> Thank you,
>
> Peter

Sadly this tool hasn't been tested since 2015-03-18 so we don't
yet know what extra clues your debug logging will reveal...

https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad/

Peter
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