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.cock@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_s...
Commit:
https://github.com/peterjc/pico_galaxy/commit/c9b77b49281974988c790a54f05c4d...
The TravisCI build is still failing, but on an unrelated change on the Galaxy dev branch.
Peter