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
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