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