diff options
Diffstat (limited to 'biology/consed/files/patch-scripts_phredPhrap')
| -rw-r--r-- | biology/consed/files/patch-scripts_phredPhrap | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/biology/consed/files/patch-scripts_phredPhrap b/biology/consed/files/patch-scripts_phredPhrap new file mode 100644 index 000000000000..5ac28e3d808a --- /dev/null +++ b/biology/consed/files/patch-scripts_phredPhrap @@ -0,0 +1,36 @@ +--- scripts/phredPhrap.orig 2007-09-26 04:02:20.000000000 +0900 ++++ scripts/phredPhrap 2007-12-11 17:32:27.000000000 +0900 +@@ -101,7 +101,7 @@ + + + # change this to reflect wherever you put the phredpar.dat file +-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat"; ++$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat"; + #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat"; + #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat"; + +@@ -207,7 +207,7 @@ + $chromatDirPath = "../chromat_dir"; + $phdDirPath = "../phd_dir"; + +-$niceExe = "/bin/nice"; ++$niceExe = "/usr/bin/nice"; + $mvExe = "/bin/mv"; + $lsExe = "/bin/ls"; + $pwdExe = "/bin/pwd"; +@@ -568,11 +568,11 @@ + + # only uncomment the following 4 lines when you have customized + # determineReadTypes.perl +-#print "\n\n--------------------------------------------------------\n"; +-#print "Now running determineReadTypes.perl...\n"; +-#print "--------------------------------------------------------\n\n\n"; ++print "\n\n--------------------------------------------------------\n"; ++print "Now running determineReadTypes.perl...\n"; ++print "--------------------------------------------------------\n\n\n"; + +-#!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n"; ++!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n"; + + + print "\n\n--------------------------------------------------------\n"; |