Hi all,
Using gzipped input files in tool functional tests (which would be decompressed by the upload tool) used to work, e.g.
https://travis-ci.org/peterjc/pico_galaxy/builds/42395911 https://github.com/peterjc/pico_galaxy/blob/539260fa4348ed454ce464e48c9dbbcc...
But with more recent versions of Galaxy this has broken, e.g.
https://travis-ci.org/peterjc/pico_galaxy/builds/44038046 https://github.com/peterjc/pico_galaxy/blob/e3064cc8f42253efd1f8eed56844d4c5...
According to the TravisCI failure, the command run was:
python /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/tools/seq_filter_by_mapping/seq_filter_by_mapping.py -i "None" -f "data" -m lax -p /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_50.dat /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_49.dat
In this case the -i argument was $input_file, and -f was its extension/datatype. Somehow the gzipped FASTQ was not found, which is why the filename is just "None" and its datatype the default "data".
My tool is sensibly returning error code 1, and:
Missing input file: 'None'
I have made some minor changes to this tool between those TravisCI tests, but the test is the same:
<tests> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="lax" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" /> </test> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="strict" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" /> </test> </tests>
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I could reproduce this on my development machine running an older Galaxy:
$ hg log | head changeset: 16732:212e1d5e9be5 branch: stable tag: tip parent: 16716:2db0fb9594d6 parent: 16731:7adac1842adf user: John Chilton jmchilton@gmail.com date: Wed Dec 10 12:20:55 2014 -0500 summary: Merged in dannon/galaxy-central/stable (pull request #602)
And again updating to the current tip,
$ hg log | head changeset: 16850:e614c7c1e0e9 tag: tip parent: 16848:1cf0af0a6324 parent: 16849:d13f2b265dbf user: Dannon Baker dannon.baker@gmail.com date: Tue Dec 16 15:48:44 2014 -0500 summary: Merged in nitesh1989/galaxy-central3 (pull request #615)
I can "fix" it by swapping the gzipped test input_file SRR639755_mito_pairs.fastq.gz to the uncompressed SRR639755_mito_pairs.fastq instead, as in this commit:
https://github.com/peterjc/pico_galaxy/commit/126e3e716965016808ec2ba3a4be3b... https://travis-ci.org/peterjc/pico_galaxy/builds/44317785
I would like to revert this workaround since the uncompressed FASTQ file is a bit large to bundle as a test case - so I hope this is simply due to an accidental regression in Galaxy itself.
Thanks,
Peter