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> 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/
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