AutoAugustus starting PASA at pipline 21
Posted: Fri Nov 20, 2015 1:02 pm
Originally posted in the old forum by Vickie on 31.01.2013 - 15:45
Hello!
I have problem usin autoaug.pl with PASA. Exactly, because of some bug in PASA, I should skip the step 20 and start pasa at step 21. But I can't do it, 'cause starting autoaug.pl with changed line 426 ($perlCmdString="perl $PASAHOME/scripts/Launch_PASA_pipeline.pl -s 21 -c alignAssembly.config -C -R -g genome.fasta ") -s 21 means starting pipeline at index 21, the autoaug.pl drops existing database in mysql, and this causes error. How should I change the script, to run PASA at needed pipeline without dropping existing database at mysql?
Best,
Vickie
Hello!
I have problem usin autoaug.pl with PASA. Exactly, because of some bug in PASA, I should skip the step 20 and start pasa at step 21. But I can't do it, 'cause starting autoaug.pl with changed line 426 ($perlCmdString="perl $PASAHOME/scripts/Launch_PASA_pipeline.pl -s 21 -c alignAssembly.config -C -R -g genome.fasta ") -s 21 means starting pipeline at index 21, the autoaug.pl drops existing database in mysql, and this causes error. How should I change the script, to run PASA at needed pipeline without dropping existing database at mysql?
Best,
Vickie