> I went to the respective file and found that the line which defines
> seq_file is commented out:
> (l.38 in def check_seq_file())
> ## seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR
> This seems to be a bug in the current version of the file.
There is clearly something amiss. In the galaxy-dist source, this line is not
> Removing the comment, the script tries to check for sequence entries in
> alignseq.loc, which I left empty before, since I didn't need aligned
> sequences in galaxy until now. Of course this results in another error:
> 'No sequences are available for 'hg19', request them by reporting this
This is the correct behavior.
> I just wanted to raise the question if this dependency is right,
> wouldn't one rather like to check for the respective build in faseq.loc
> (unfortunately the file format is different, it doesn't contain the seq
> in the first column).
Yes, faseq.loc should be used. The use of alignseq.loc is a historical artifact
that we haven't fixed yet. If you're inclined to fix it, we'd be happy to
incorporate the changes into the code base.
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