This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository surankco.
commit 910d58fda37b2bfcc9c554fbf5c9c031716f933f Author: Andreas Tille <[email protected]> Date: Thu Mar 31 00:34:53 2016 +0200 Adapt pathes to Debian locations --- debian/patches/jar_path.patch | 112 ++++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 113 insertions(+) diff --git a/debian/patches/jar_path.patch b/debian/patches/jar_path.patch new file mode 100644 index 0000000..a260e58 --- /dev/null +++ b/debian/patches/jar_path.patch @@ -0,0 +1,112 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Thu, 24 Mar 2016 14:03:34 +0100 +Description: Adapt pathes to Debian locations + +--- a/surankco-feature ++++ b/surankco-feature +@@ -22,12 +22,12 @@ DEBUGGING <- FALSE + + + # sources and libraries +-source(paste(script.path, '/r/parameter.R', sep="")) +-source(paste(script.path, '/r/feature.R', sep="")) +-source(paste(script.path, '/r/functions.R', sep="")) +-source(paste(script.path, '/r/coverage.R', sep="")) +-source(paste(script.path, '/r/covcurv.R', sep="")) +-source(paste(script.path, '/r/import.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/parameter.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/feature.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/functions.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/coverage.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/covcurv.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/import.R', sep="")) + loadPackages(c("optparse","parallel"), quietly=TRUE) + + +@@ -58,7 +58,7 @@ for (i in 1:nrow(files)){ + paste("-Xms", parameters$memory, "G", sep=""), + paste("-Xmx", parameters$memory, "G", sep=""), + "-Dcom.ibm.tools.attach.enable=no -jar", +- paste(script.path, "surankco.jar", sep="/"), ++ paste("/usr/share/java", "surankco.jar", sep="/"), + input.file.assembly[i], # args[0] Assembly File + input.file.quality[i], # args[1] Fasta/Qual File + output.file.features[i], # args[2] Tmp Feature Output File +--- a/surankco-prediction ++++ b/surankco-prediction +@@ -23,10 +23,10 @@ DEBUGGING <- FALSE + + + # sources and libraries +-source(paste(script.path, '/r/parameter.R', sep="")) +-source(paste(script.path, '/r/import.R', sep="")) +-source(paste(script.path, '/r/rf.R', sep="")) +-source(paste(script.path, '/r/voting.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/parameter.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/import.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/rf.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/voting.R', sep="")) + # ... + loadPackages(c("optparse","randomForest"), quietly=TRUE) + +@@ -75,4 +75,4 @@ write.table(results, file=parameters$out + sep="\t", dec = ".", col.names=TRUE, row.names=FALSE) + + # done +-cat("surankco-prediction calculations done\n") +\ No newline at end of file ++cat("surankco-prediction calculations done\n") +--- a/surankco-score ++++ b/surankco-score +@@ -22,10 +22,10 @@ DEBUGGING <- FALSE + + + # sources and libraries +-source(paste(script.path, '/r/parameter.R', sep="")) +-source(paste(script.path, '/r/scores.R', sep="")) +-source(paste(script.path, '/r/expofits.R', sep="")) +-source(paste(script.path, '/r/import.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/parameter.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/scores.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/expofits.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/import.R', sep="")) + loadPackages(c("optparse","MASS"), quietly=TRUE) + + +@@ -68,7 +68,7 @@ for (i in 1:nrow(files)){ + } + + # filter alignments +- filter.call <- paste(paste(script.path, "/r/pslMatchFilter", sep=""), ++ filter.call <- paste(paste('/usr/lib/R/site-library/surankco', "/pslMatchFilter", sep=""), + output.file.psl, output.file.filter) + + if (DEBUGGING){ +@@ -97,7 +97,7 @@ for (i in 1:nrow(files)){ + paste("-Xms", parameters$memory, "G", sep=""), + paste("-Xmx", parameters$memory, "G", sep=""), + "-cp", +- paste(script.path, "surankco.jar", sep="/"), ++ paste("/usr/share/java", "surankco.jar", sep="/"), + "de.rki.ng4.surankco.scoring.Main", + output.file.pretty, + output.file.scores) +--- a/surankco-training ++++ b/surankco-training +@@ -22,11 +22,11 @@ DEBUGGING <- FALSE + + + # sources and libraries +-source(paste(script.path, '/r/parameter.R', sep="")) +-source(paste(script.path, '/r/import.R', sep="")) +-source(paste(script.path, '/r/rf.R', sep="")) +-source(paste(script.path, '/r/scores.R', sep="")) +-source(paste(script.path, '/r/expofits.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/parameter.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/import.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/rf.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/scores.R', sep="")) ++source(paste('/usr/lib/R/site-library/surankco', '/expofits.R', sep="")) + loadPackages(c("optparse","MASS","randomForest"), quietly=TRUE) + + diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..6f2ecdc --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +jar_path.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/surankco.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
