Brian Haas also behind this Splice Alignment tool.
PASA has quite alot of parts and it could almost be seen as a mini-pipeline. THe canonical command for running it on the marvin cluster is:
Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2
- -c is a configuration file which you, the user, needs to set up. The database name you choose for the analysis needs to be specified in this.
- -C is for creating a new database, if there is one there already, the command will fail.
- --CPU is for the number of threads.
- The PASA mysql user requires full privileges so it can create databases, which it apparently does for every analysis.
- these privileges must also exist for '%', so that all the nodes can also do this.
- the issue of a key being too long for mysql was corrected by replacing 1000 with 500 in this line.
gene_id varchar(1000) default NULL,
in the $PASAHOME/schema/cdna_alignment_mysqlschema file on line 174, which was also an issue back in 2013 (see links section).
- Yours truly posing a question in May 2013! here.