Hi list,

I’ve been trying to write functional tests for a tool that produces BAM
files as output. The tests run fine when using planemo locally,
but not on the testtoolshed or on machines that do not have samtools
installed.
Apparently galaxy automatically tries to convert BAM to SAM to compare
the output line by line, and so this fails. Surprisingly this is also true
when
comparing by size.
This is the error:


Tool id: bowtieForSmallRNA
Tool version: bowtieForSmallRNA
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.0)
Stderr:

Traceback:
Traceback (most recent call last):
  File 
"/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 270, 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/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam
v. 
/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/tmpQMbAfNoutput.bam
)
Converting local (test-data) bam to sam failed: (cmd=[samtools view -h
-o 
"/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/local_bam_converted_to_sam_8Ym0af.sam"
"/tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam"],
stdout=[], stderr=[/bin/sh: 1: samtools: not found
])

Should samtools perhaps be added to the list of tools required for running
galaxy?

Best,
Marius
​
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