Thanks John,

That sounds like quite a subtle root cause - well done. I've
reverted my workaround and the TravisCI tests pass again:

https://github.com/peterjc/pico_galaxy/commit/265bf7f62ad4fa7c8557a6bfa5af65a687b31b46
https://travis-ci.org/peterjc/pico_galaxy/builds/44334522

Regards,

Peter


On Wed, Dec 17, 2014 at 2:45 PM, John Chilton <jmchil...@gmail.com> wrote:
> 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
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