Hello,
This package is one of the closest that we have on our radar to suit
virologists, to I went for CATCH from the broad institute at
https://github.com/broadinstitute/catch . Conda has it already, does not
surface on bio.tools, though.
Testing takes quite a while (~15mins) and the few that fail seem to
depend on viral sequence data that cannot be downloaded. So, I consider
the package functional, but don't really know what to do with the test
that fail because they have to fail.
Are there suggestions from your sides what to do about them?
On another note, when I just wanted to inject it all to salsa, it failed
to create the pristine-tar:
> [...]
That file is small
$ du -sh catch/datasets/data/achimota_rubulavirus_1.fasta.gz
8.5K catch/datasets/data/achimota_rubulavirus_1.fasta.gz
so there is no need for git-lsf in the first place, right?
Yes, no need. It looks weird on first look though
If you have the sources in a non-git repository could you do something like:
$ dpkg-source -b .
$ cd ..
$ gbp import-dsc --pristine-tar <your .dsc file>
And see what you get?
> <snip>
> Huge test log
> </snip>
Some of these don't work due to a missing .tsv file, others because they try to access internet w/ urllib, few others due to a missing fasta file.
But it's difficult to debug till we have a repository in salsa to look stuff up and fix, so if you could commit, it'd be easy to move forward
Nilesh