To recap, in the next release of Galaxy, there will not be a copy of the
sequence parsing code like lib/galaxy_utils/sequence/fastq.py - see
this pull request: https://github.com/galaxyproject/galaxy/pull/3551

Both Galaxy itself, and any tools needing it, will depend on the now
separately packaged galaxy_sequence_utils library, source code now
here:

https://github.com/galaxyproject/sequence_utils

The original version of this is available on the Tool Shed:

https://toolshed.g2.bx.psu.edu

The library is now available on PyPI too:

https://pypi.python.org/pypi/galaxy_sequence_utils/

This code has been updated and now does "import six" as part of
work to make sure it can be used on Python 2 and Python 3, and
it includes support for compressed FASTQ files.

My TravisCI tool tests are passing again using both Galaxy's stable
and dev branches.

Peter

On Wed, Feb 1, 2017 at 11:20 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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
___________________________________________________________
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/

Reply via email to