[Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed May 21 08:34:52 UTC 2008


------- Comment #17 from biopython-bugzilla at maubp.freeserve.co.uk  2008-05-21 04:34 EST -------
The os.path.exists(...) check in Biopython should be easy to fix, probably by
the user specifying the exe name without quotes and biopython adding the quotes
when building the command line.

For specifying the NCBI database locations, have you set the database folder
using NCBI.ini yet?  I'm not sure if it will work if the INI file is in the
BLAST directory as the NCBI documentation says it should go in the Windows
directory (which you don't have write access to).  Perhaps anywhere on the path
will work.  See ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blast.html

There is also the option of using relative paths...

You might get more success talking to the machine administrator and asking them
to install BLAST for you?

The good news is my home internet connection is up and running, so I may be
able to do a little investigation on this issue now (time permitting).

Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list