[med-svn] [surankco] 03/06: Adapt pathes to Debian locations

[Andreas Tille]

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tille pushed a commit to branch master
in repository surankco.

commit 910d58fda37b2bfcc9c554fbf5c9c031716f933f
Author: Andreas Tille <tille at debian.org>
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 <tille at debian.org>
+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

-- 
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