Torsten, Thanks -- I had missed noting legacy_blast.pl. After editing the script to reflect my local install's DEFAULT_PATH for blast it seems to be working at a direct command line level (i.e., I tested a couple of queries and they worked). So setting up a symlink sounds like the way to go -- I'm rusty on those, and am working in Mac OS X, so some reading is in order. Thanks again!
- Guy On 3/16/10, Torsten Seemann wrote: >Guy, > >> Is there a version of (or suggested edits to) Artemis to make it compatible >> with NCBI's BLAST+? I edited setup_dbs.sh to deal with makeblastdb replacing >> formatdb, and that seems to have worked. But it strikes me that any internal >> calls must use the old blastall command, and I'm not sure how (or even if) >> that can be addressed ... >> Or am I better off starting over after downloading the old version of BLAST? > >Databases created with 'formatdb' (BLAST) can be used by the BLAST+ >search tools. > >A possible work-around for you would be to use the "legacy_blast.pl" >script that comes with BLAST+. It takes the BLAST cmdline options and >translates them to a call to BLAST+ tools. If you renamed it >"blastall" with a symlink, it might just work? > >--Torsten Seemann >--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash >University, AUSTRALIA _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
