So the PR that broke your tools is probably here https://github.com/
galaxyproject/galaxy/pull/3364/files. That pull request removed Galaxy from
the Python path of Galaxy tools - this gives tools a much cleaner
environment and prevents certain conflicts between Conda and Galaxy.

As part of that PR, there is a list of Galaxy tools in
lib/galaxy/tools/__init__.py that still get setup with Galaxy's Python
environment. This includes many random devteam and even an IUC tool - I've
added something to the list even though one ancient version of tool shed
tool required it years ago and it has since been updated. I would open a PR
to add the tool id of any of your tools that have been published to the
tool shed and require these tools to this list. You can target it against
17.01 ideally and then we can merge that into dev.

This behavior can be reverted - there is a config option that is documented
pretty well in the PR but I missed named it in the sample (fixing it with
https://github.com/galaxyproject/galaxy/pull/3521/files).

Hopefully this helps and thanks for the bug report!

-John


On Tue, Jan 31, 2017 at 7:08 AM Peter Cock <p.j.a.c...@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 <nsora...@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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> >
> >
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