ODoSE not working properly. Does an ODoSE manual exist?

Question: ODoSE not working properly. Does an ODoSE manual exist?

2.9 years ago by

dago • 0

dago • 0 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 • 692 views

ADD COMMENT • link •

modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by dago • 0

2.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 2.9 years ago by dago • 0

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 REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »