# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Anton Nekrutenko <anton@bx.psu.edu> # Date 1289851499 18000 # Node ID 9a7482206be274678079271331171600a2023b03 # Parent 3868982a4eff5036f13650ab303e0b9a4fb30da8 Tweaks to taxonomy tools --- a/tools/taxonomy/t2ps_wrapper.py +++ b/tools/taxonomy/t2ps_wrapper.py @@ -59,7 +59,7 @@ except OSError, e: # Convert PS to PDF try: - ps2pdf_cmd = 'ps2pdf %s %s' % ( ps_file.name, pdf_file ) + ps2pdf_cmd = 'pstopdf %s -o %s' % ( ps_file.name, pdf_file ) retcode = subprocess.call( ps2pdf_cmd, shell=True ) if retcode < 0: print >>sys.stderr, "Execution of ps2pdf terminated by signal", -retcode --- a/scripts/taxonomy/processTaxonomy.sh +++ b/scripts/taxonomy/processTaxonomy.sh @@ -11,7 +11,7 @@ echo "Sorting gi2tax files..." sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp echo "Removing parenthesis from names.dmp" -cat names.dmp | sed s/\(/_/g | sed s/\)/_/g > names.temporary +cat names.dmp | sed s/[\(\)\'\"]/_/g > names.temporary mv names.dmp names.dmp.orig mv names.temporary names.dmp