This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository giira.
commit 692c173f93a2aaf70c1b1b97335b43d60145cc59 Author: Andreas Tille <[email protected]> Date: Mon Jan 9 12:04:25 2017 +0100 Adapt patches --- debian/patches/fix_non-ascii_characters.patch | 15 --------------- debian/patches/fix_scripts-path.patch | 12 ++++++------ debian/patches/remove_cplex_code.patch | 6 +++--- debian/patches/series | 1 - debian/rules | 1 + 5 files changed, 10 insertions(+), 25 deletions(-) diff --git a/debian/patches/fix_non-ascii_characters.patch b/debian/patches/fix_non-ascii_characters.patch deleted file mode 100644 index 400d034..0000000 --- a/debian/patches/fix_non-ascii_characters.patch +++ /dev/null @@ -1,15 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Updated: Sat, 08 Feb 2014 14:38:38 +0100 -Description: Remove non-ASII character from comment - ---- a/src/types/Rna.java -+++ b/src/types/Rna.java -@@ -17,7 +17,7 @@ public class Rna { - - public double quality; - -- public Vector<Object[]> contigsMappedOn = new Vector<Object[]>(); // contains several Arrays รก: [contig, alignPos, cigarString, mapQual,spliceInfo,mismatchInfo,direcInfo] (one for each hit) -+ public Vector<Object[]> contigsMappedOn = new Vector<Object[]>(); // contains several Arrays: [contig, alignPos, cigarString, mapQual,spliceInfo,mismatchInfo,direcInfo] (one for each hit) - - public int isMulti; // indicator if this read is an ambiguous read - diff --git a/debian/patches/fix_scripts-path.patch b/debian/patches/fix_scripts-path.patch index c0ea1ca..940929e 100644 --- a/debian/patches/fix_scripts-path.patch +++ b/debian/patches/fix_scripts-path.patch @@ -14,7 +14,7 @@ Description: Hardcode path to Python helper scripts --- a/src/geneFinder/ReadInParameters_GeneFinder.java +++ b/src/geneFinder/ReadInParameters_GeneFinder.java -@@ -357,7 +357,7 @@ public class ReadInParameters_GeneFinder +@@ -379,7 +379,7 @@ public class ReadInParameters_GeneFinder try { String decodedPath = URLDecoder.decode(path, "UTF-8"); String scriptPath = decodedPath.substring(0,decodedPath.length()-9); @@ -25,12 +25,12 @@ Description: Hardcode path to Python helper scripts } --- a/src/geneFinder/Giira.java +++ b/src/geneFinder/Giira.java -@@ -43,7 +43,7 @@ public class Giira { - - try { +@@ -45,7 +45,7 @@ public class Giira { String decodedPath = URLDecoder.decode(path, "UTF-8"); -- String scriptPath = decodedPath.substring(0,decodedPath.length()-9); + String[] pathArr = decodedPath.split("/"); + int lengthName = pathArr[pathArr.length-1].length(); +- String scriptPath = decodedPath.substring(0,decodedPath.length()-lengthName); + String scriptPath = "/usr/share/giira/"; + //String scriptPath = decodedPath.substring(0,decodedPath.length()-9); //System.out.println("Path of Giira: " + decodedPath); - classPath = ""; diff --git a/debian/patches/remove_cplex_code.patch b/debian/patches/remove_cplex_code.patch index d7821df..cfddf19 100644 --- a/debian/patches/remove_cplex_code.patch +++ b/debian/patches/remove_cplex_code.patch @@ -8,7 +8,7 @@ Last-Updated: 2014-02-08 Forwarded: no --- a/src/geneFinder/ReadInParameters_GeneFinder.java +++ b/src/geneFinder/ReadInParameters_GeneFinder.java -@@ -242,9 +242,8 @@ public class ReadInParameters_GeneFinder +@@ -249,9 +249,8 @@ public class ReadInParameters_GeneFinder GeneFinder.useGLPK = true; inputText += "Using glpk for ambiguous read optimization.\n"; } else{ @@ -20,7 +20,7 @@ Forwarded: no } } else if(arg.equals("-mem")){ GeneFinder.memForCplex = Integer.parseInt(args[i+1]); -@@ -376,7 +375,8 @@ public class ReadInParameters_GeneFinder +@@ -398,7 +397,8 @@ public class ReadInParameters_GeneFinder GeneFinder.noAmbiOpti = false; } if(!foundOptiMethod){ @@ -30,7 +30,7 @@ Forwarded: no } if(!foundSolveOn){ GeneFinder.optiSolve = true; -@@ -462,8 +462,6 @@ public class ReadInParameters_GeneFinder +@@ -545,8 +545,6 @@ public class ReadInParameters_GeneFinder " \n -haveSam [samfileName]: if a sam file already exists, provide the name, else a mapping is performed. NOTE: the sam file has to be sorted according to read names! \n" + " \n -nT [numberThreads] : specify the maximal number of threads that are allowed to be used, DEFAULT: 1 \n" + " \n -mT [tophat/bwa/bwasw] : specify desired tool for the read mapping, DEFAULT: tophat \n" + diff --git a/debian/patches/series b/debian/patches/series index 2eb66d5..6222007 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,2 @@ remove_cplex_code.patch -fix_non-ascii_characters.patch fix_scripts-path.patch diff --git a/debian/rules b/debian/rules index 387628d..3585591 100755 --- a/debian/rules +++ b/debian/rules @@ -5,6 +5,7 @@ SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') export JAVA_HOME=/usr/lib/jvm/default-java +export LC_ALL=C.UTF-8 %: dh $@ --with javahelper -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/giira.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
