Hi Nilesh, Thank you tons for thinking along.
On 27.07.21 17:47, Nilesh Patra wrote:
On Tue, 27 Jul, 2021, 9:02 pm Steffen Möller, <[email protected] <mailto:[email protected]>> wrote: 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 <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 Any idea? 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
It took me a bit but. Too long. The answer is that git does not lose the sensation of a file being a git lfs reference even when you download a tar.gz. For some reason I had expected that all genomes were truly gzipped fasta files, but no, they were still references. Maybe I had inadvertently transformed a few to what they point to during a first build and that is why I then did not find the issue a bit earlier. The import of pristine-tar has worked after removing .gitattributes, but then the git lfs references were still in the tarball and the upstream branch. pristine-tar could be pushed, but then the other branches would trigger git lfs errors when pushed to salsa. Only after having all fasta.gz lfs files removed, the upload went smoothly and you all now find this on https://salsa.debian.org/med-team/broad-catch . Tests seem to do just as fine as before, still. Best, Steffen
