This went smoother today, and has served to refresh some of the
details of how the Galaxy's venv etc all work.

In my TravisCI setup for tool testing I currently "manually" install
the tool dependencies, and thus am using pip with the same URL
as the Tool Shed package:

pip install 
http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz

Commit:

https://github.com/peterjc/pico_galaxy/commit/c9b77b49281974988c790a54f05c4d1ff81b0904

The TravisCI build is still failing, but on an unrelated change
on the Galaxy dev branch.

Peter

On Wed, Feb 1, 2017 at 9:46 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Thanks John - that could explain what's going wrong and offers
> another approach to fixing my TravisCI testing - setting:
>
> preserve_python_environment  = legacy_and_local
>
> or:
>
> preserve_python_environment = always
>
> (Despite several attempts I didn't hit on a nice way to get the
> galaxy_sequence_utils installed nicely via a "manual install",
> one day I will switch my TravisCI testing to use BioConda)
>
> I am hoping to get my TravisCI builds passing again today...
>
> Peter
>
> On Tue, Jan 31, 2017 at 5:27 PM, John Chilton <jmchil...@gmail.com> wrote:
>> 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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