Question: ODoSE not working properly. Does an ODoSE manual exist?
0
gravatar for dago
2.1 years ago by
dago0
dago0 wrote:

I am struggling with ODoSE since a while with no success.

I cannot find a way so use the select genomes function (that's what I see).

Also, I tried to upload  a .faa of the genomes I am working with, this worked. If I then try to use the function "Identify core.." I always get the same error:

<class 'zipfile.BadZipfile'>
Automatic bug submission reported: BadZipfile @ /usr/lib/python2.7/zipfile.py:_RealGetContents
An error occurred
Traceback (most recent call last):
  File "/work/odosenl/galaxy-dist/tools/odosenl/wrapper.py", line 32, in <module>
    MODULE.main(sys.argv[3:])
  File "/work/odosenl/odose.nl/run_orthomcl.py", line 448, in main
    proteome_files = extract_archive_of_files(args.proteinzip, temp_dir)
  File "/work/odosenl/odose.nl/shared.py", line 90, in extract_archive_of_files
    read_handle = ZipFile(archive_file, mode='r')
  File "/usr/lib/python2.7/zipfile.py", line 714, in __init__
    self._GetContents()
  File "/usr/lib/python2.7/zipfile.py", line 748, in _GetContents
    self._RealGetContents()
  File "/usr/lib/python2.7/zipfile.py", line 763, in _RealGetContents
    raise BadZipfile, "File is not a zip file"
BadZipfile: File is not a zip file

Is there any manual/Tutorial for this program, I looked a lot around, but I could not find any.

Thanks

odose software error manual • 506 views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson24k • written 2.1 years ago by dago0
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

A google with ODoSE bioinformatics as the query term brings up the author's Github repository plus many other information sources.

If working at the ODeSE public Galaxy server, contact information can be found here along with a manual link: https://wiki.galaxyproject.org/PublicGalaxyServers#ODoSE

Good luck with your project! Jen, Galaxy team

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson24k

Thanks I look into it, but I could not find any manual/tutorial or similar

ADD REPLYlink written 2.1 years ago by dago0

There is a manual link clearly labeled in the wiki section for ODoSE above. If for some reason you are having trouble with it, contacting the owners of the instance is the next step.

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson24k
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