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/a74d32014b0512613042c... 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.cock(a)googlemail.com&gt; 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/539260fa4348ed454ce464e48c9db... > > 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/e3064cc8f42253efd1f8eed56844d... > > 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 <jmchilton(a)gmail.com&gt; > 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(a)gmail.com&gt; > 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/126e3e716965016808ec2ba3a4b... > 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/