It would also be nice to have gops in Conda, either Bioconda or iuc channel. Cheers, Nicola On 31/01/17 15:01, Martin Čech wrote:
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 <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@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 <nsoranzo@tiscali.it <mailto:nsoranzo@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 >> ___________________________________________________________ >> 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/ > > ___________________________________________________________ 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/
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