#Setting up variables
#sloc='/Volumes/Bay3/Software/ap11_samifier-master/dist/'
#sloc='/Applications/ap11_samifier-master/dist/'
sloc='/Volumes/Bay3/Software/ap11_samifier-master/dist/'
#timestamp
date=!date +%m%d_%H%M
!java -jar {sloc}samifier.jar \
-r /Volumes/web/cnidarian/F003766.mzid \
-m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt \
-g /Volumes/web/cnidarian/ets_v9_o.gff \
-c /Volumes/web/cnidarian/v9_multi \
-o /Volumes/web/cnidarian/Cg_samifier_out{date} \
-l /Volumes/web/cnidarian/log_{date} \
-b /Volumes/web/cnidarian/Cg_{date}.bed
Start document End document!
#Setting up variables
#sloc='/Volumes/Bay3/Software/ap11_samifier-master/dist/'
#sloc='/Applications/ap11_samifier-master/dist/'
sloc='/Volumes/Bay3/Software/ap11_samifier-master/dist/'
#timestamp
date=!date +%m%d_%H%M
!java -jar {sloc}samifier.jar \
-r /Volumes/web/cnidarian/F003766.mzid \
-m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt \
-g /Volumes/web/cnidarian/ets_v9_bb.gff \
-c /Volumes/web/cnidarian/v9_multi \
-o /Volumes/web/cnidarian/Cg_samifier_out{date} \
-l /Volumes/web/cnidarian/log_{date} \
-b /Volumes/web/cnidarian/Cg_{date}.bed
Start document End document!
!head /Volumes/web/whale/wiki_test_cases/pipeline_glimmer.gff
##gff-version 3 NC_009802 Glimmer gene 1 1311 16.88 + 0 Name=orf00002;ID=orf00002; NC_009802 Glimmer CDS 1 1311 16.88 + 0 Name=orf00002;Parent=orf00002; NC_009802 Glimmer gene 1319 1465 1.61 + 0 Name=orf00003;ID=orf00003; NC_009802 Glimmer CDS 1319 1465 1.61 + 0 Name=orf00003;Parent=orf00003; NC_009802 Glimmer gene 1465 2532 15.89 + 0 Name=orf00004;ID=orf00004; NC_009802 Glimmer CDS 1465 2532 15.89 + 0 Name=orf00004;Parent=orf00004; NC_009802 Glimmer gene 2550 4859 16.58 + 0 Name=orf00005;ID=orf00005; NC_009802 Glimmer CDS 2550 4859 16.58 + 0 Name=orf00005;Parent=orf00005; NC_009802 Glimmer gene 4878 5474 16.37 + 0 Name=orf00006;ID=orf00006;
!head /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt
CGI_10027970 CGI_10027970 CGI_10027970