On Tue, Jan 31, 2017 at 7:08 AM Peter Cock <p.j.a.cock@googlemail.com> wrote:

Thanks Nicola,

I didn't spot the missing slash, but planemo lint did - for anyone
else copy-and-pasting:

<requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>

For anyone not yet using BioConda with Galaxy, there is also a Tool
Shed entry here:

https://toolshed.g2.bx.psu.edu/view/iuc/package_galaxy_sequence_utils_1_0_1/

I am therefore adding this to my tool_dependencies.xml files:

<package name="galaxy_sequence_utils" version="1.0.1">
<repository name="package_galaxy_sequence_utils_1_0_1" owner="iuc" />
</package>

I still need to work out how best to make this available under TravisCI,
given I am not currently using BioConda for the dependencies.

@IUC: Should this also be released on PyPI for easy install via pip?

Peter

On Tue, Jan 31, 2017 at 11:15 AM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
> Hi Peter,
> adding
>
> <requirement type="package"
> version="1.0.1">galaxy_sequence_utils<requirement>
>
> to each of these tools should solve the problem, there is a Bioconda package
> which provides the Python library:
>
> https://anaconda.org/bioconda/galaxy_sequence_utils
>
> Cheers,
> Nicola
>
>
> On 31/01/17 10:39, Peter Cock wrote:
>>
>> Hi all,
>>
>> A few of my tools have for a long time used Galaxy's own parsing
>> functionality in order to avoid an external dependency. Lately
>> this has stopped working on my TravisCI testing with planemo
>> using the Galaxy dev branch (the stable master branch is fine):
>> e.g.
>>
>> https://travis-ci.org/peterjc/pico_galaxy/builds/196655736
>>
>> The tools fail with things like:
>>
>> | from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
>> | ImportError: No module named galaxy_utils.sequence.fasta
>>
>>
>> or:
>>
>> | from galaxy_utils.sequence.fastq import fastqReader
>> | ImportError: No module named galaxy_utils.sequence.fastq
>>
>> Is this a temporary regression in Galaxy, or a deliberate change?
>> Do the tools need to do something to explicit have access to the
>> Galaxy Python library, or are they now considered private?
>> If so, I can update these tools to use an explicit dependency
>> for parsing FASTA and FASTQ (e.g. Biopython).
>>
>> Thanks,
>>
>> Peter
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