Hey Peter, Thanks for the very detailed bug report - it really helped track things down.
I have pushed a fix to next-stable and default (the bug never reached stable). https://bitbucket.org/galaxy/galaxy-central/commits/a74d32014b0512613042c2a44d0b946703a1fbcd The commit also includes a test case so hopefully this won't break again. -John On Wed, Dec 17, 2014 at 6:56 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > 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/539260fa4348ed454ce464e48c9dbbccca22a012/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml > > 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/e3064cc8f42253efd1f8eed56844d4c54645072e/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml > > 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> > > -- > > 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 <jmchil...@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.ba...@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/126e3e716965016808ec2ba3a4be3b1075a2ebbf > 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 > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
