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
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
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
Hi folks,
the two of the Galaxy-born libraries have sources at our GitHub:
https://github.com/galaxyproject/gops
https://github.com/galaxyproject/sequence_utils
Any improvements or PyPI-readiness work are welcome.
Best,
Martin
On Tue, Jan 31, 2017 at 7:08 AM Peter Cock
Thanks Nicola,
I didn't spot the missing slash, but planemo lint did - for anyone
else copy-and-pasting:
galaxy_sequence_utils
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
Hi Peter,
adding
version="1.0.1">galaxy_sequence_utils
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
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.
