search

dgrtwo / OASIS

Optimized Annotation System for Insertion Sequences
10 stars 4 forks source link

full path to the blastall and formatdb #1

Open BernardoBello opened 11 years ago

BernardoBello commented 11 years ago

Hi,

I'm trying to use your software but stopped at step of setting 'full path to the blastall and formatdb executables on your computer'.

Since 'The original standalone BLAST package based on NCBI C-toolkit (legacy blast) is depreciated.' (http://www.ncbi.nlm.nih.gov/books/NBK52640/), it would be nice to know if it is still possible to use OASIS with the new BLAST+.

What I mean is that I have BLAST+ installed but blastall and formatdb are not in my computer since BLAST+ works in a different way.

Hope I explained well. Maybe I'm wrong since I'm starting with UNIX.

Thank you. Sincerely, Bernardo

andrew-niaid commented 8 years ago

Sorry for bumping an old issue, but I just got OASIS running on a modern (CentOS 7.2) system and thought I'd leave my solution for anyone searching.

OASIS does indeed require legacy blast, I used http://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/LATEST/blast-2.2.26-x64-linux.tar.gz on CentOS 7 and it worked fine for me.

OASIS also requires an old version of biopython. Support for legacy blast in biopython was removed in version 1.64, so you will need to install biopython-1.63 so OASIS can interfaces with legacy blast. I used http://www.biopython.org/DIST/biopython-1.63.tar.gz.