Problem with swga count

[Rcoppee]

Dear swga community,

I have a problem when I use swga.

First of all, I didn't install virtualenv, the archive seems to have some problems. However, I success to install swga, and the swga init command works properly (which allows me to receive the foreground and background genomes. Two files are created.

Now, when I run the swga count command, I have a series of errors:

swga count, v0.4.4
  - force: False
  - max_dimer_bp: 3
  - exclude_threshold: 1
  - min_size: 5
  - input: None
  - min_fg_bind: 237
  - max_bg_bind: 21128
  - max_size: 12
Traceback (most recent call last):
  File "/home/maintenance-gg/.local/bin/swga", line 8, in <module>
    sys.exit(main())
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/main.py", line 81, in main
    setup_and_run(cmd_class, args.command, remaining)
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/main.py", line 49, in setup_and_run
    cmd.run()
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/commands/count.py", line 27, in run
    self.count_kmers()
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/commands/count.py", line 85, in count_kmers
    fg = swga.kmers.count_kmers(k, self.fg_genome_fp, output_dir)
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/kmers.py", line 42, in count_kmers
    cmdarr = [swga.utils.dsk(), genome_fp, str(k), '-o', out, '-t', str(threshold)]
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/utils.py", line 93, in dsk
    return _get_resource_file('dsk')
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/utils.py", line 72, in _get_resource_file
    swga.error("Could not find `{}': try re-installing swga.".format(rs))
  File "/home/maintenance-gg/.local/lib/python2.7/site-packages/swga/__init__.py", line 25, in error
    raise SWGAError(msg)
swga.SWGAError: Could not find `dsk': try re-installing swga.

I uninstall dsk, then properly install it, but the error remains.
Do you know the origin of this error?

Thank you in advance!

Regards,

Asternosis

[SarahNadeau]

In case anyone else runs into this, I got the same error and I think I it comes from swga looking for dsk in the wrong place.

swga/swga/utils.py

Line 63 in b36cefa

_rs = os.path.join(sys.prefix, 'bin', rs)

I have swga installed in a Docker image, so I fixed this issue by copying dsk to where swga expects it in my Dockerfile:

cp /usr/local/bin/dsk /usr/bin/dsk

Now swga count runs file.

[SarahNadeau]

Same thing applies for set_finder from cliquer, which is needed for swga find_sets:

cp /usr/local/bin/set_finder /usr/bin/set_finder