Author: osallou Date: 2014-08-19 10:32:57 +0000 (Tue, 19 Aug 2014) New Revision: 17793
Added: trunk/packages/babraham/fastqc/trunk/debian/patches/set_configuration_path Modified: trunk/packages/babraham/fastqc/trunk/debian/README.Debian trunk/packages/babraham/fastqc/trunk/debian/changelog trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch trunk/packages/babraham/fastqc/trunk/debian/patches/series Log: fix Configuration dir loading Modified: trunk/packages/babraham/fastqc/trunk/debian/README.Debian =================================================================== --- trunk/packages/babraham/fastqc/trunk/debian/README.Debian 2014-08-19 10:26:21 UTC (rev 17792) +++ trunk/packages/babraham/fastqc/trunk/debian/README.Debian 2014-08-19 10:32:57 UTC (rev 17793) @@ -9,7 +9,12 @@ each file without launching a user interface. This would allow FastQC to be run as part of an analysis pipeline. +Configuration +------------- +Configuration files have been placed in /etc/fastqc/Configuration + + Running FastQC Interactively ---------------------------- Modified: trunk/packages/babraham/fastqc/trunk/debian/changelog =================================================================== --- trunk/packages/babraham/fastqc/trunk/debian/changelog 2014-08-19 10:26:21 UTC (rev 17792) +++ trunk/packages/babraham/fastqc/trunk/debian/changelog 2014-08-19 10:32:57 UTC (rev 17793) @@ -1,3 +1,10 @@ +fastqc (0.11.2+dfsg-1) UNRELEASED; urgency=medium + + * Fix Configuration dir loading (Closes: #756296). + Files are in directroy /etc/fastqc/Configuration + + -- Olivier Sallou <[email protected]> Tue, 19 Aug 2014 09:06:07 +0200 + fastqc (0.11.2+dfsg-1) unstable; urgency=medium * New upstream release Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch =================================================================== --- trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch 2014-08-19 10:26:21 UTC (rev 17792) +++ trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch 2014-08-19 10:32:57 UTC (rev 17793) @@ -1,15 +1,17 @@ From: Steffen Moeller <[email protected]> Subject: Simplyfy installation by creating a Makefile +Index: FastQC/Makefile +=================================================================== --- /dev/null -+++ b/Makefile -@@ -0,0 +1,19 @@ ++++ FastQC/Makefile +@@ -0,0 +1,21 @@ + +all: fastqc.jar + +fastqc.jar: + javac -source 1.6 -target 1.6 -cp /usr/share/java/commons-math3.jar:/usr/share/java/sam.jar:/usr/share/java/jbzip2.jar `find uk -name "*.java"` `find net -name "*.java"` -+ jar cf fastqc.jar `find uk -name "*.class" -o -name "*.png"` ++ jar cf fastqc.jar `find uk -name "*.class" -o -name "*.png"` `find net -name "*.class" -o -name "*.png"` Templates + +DESTDIR= +PREFIX=/usr @@ -19,9 +21,9 @@ + chmod +x $(DESTDIR)$(PREFIX)/bin/fastqc + mkdir -p $(DESTDIR)$(PREFIX)/share/fastqc/ + cp -a fastqc.jar $(DESTDIR)$(PREFIX)/share/fastqc/ -+ cp -r Configuration Templates Help $(DESTDIR)$(PREFIX)/share/fastqc/ ++ cp -r Templates Help $(DESTDIR)$(PREFIX)/share/fastqc/ ++ mkdir -p $(DESTDIR)/etc/fastqc ++ cp -r Configuration $(DESTDIR)/etc/fastqc/ + +clean: + find . -name "*.jar" -o -name "*.class" | xargs -r rm -+ -+.PHONY: all install Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/series =================================================================== --- trunk/packages/babraham/fastqc/trunk/debian/patches/series 2014-08-19 10:26:21 UTC (rev 17792) +++ trunk/packages/babraham/fastqc/trunk/debian/patches/series 2014-08-19 10:32:57 UTC (rev 17793) @@ -1,3 +1,4 @@ Makefile.patch fastqc.patch fix-help-call.patch +set_configuration_path Added: trunk/packages/babraham/fastqc/trunk/debian/patches/set_configuration_path =================================================================== --- trunk/packages/babraham/fastqc/trunk/debian/patches/set_configuration_path (rev 0) +++ trunk/packages/babraham/fastqc/trunk/debian/patches/set_configuration_path 2014-08-19 10:32:57 UTC (rev 17793) @@ -0,0 +1,70 @@ +Index: FastQC/uk/ac/babraham/FastQC/Modules/ModuleConfig.java +=================================================================== +--- FastQC.orig/uk/ac/babraham/FastQC/Modules/ModuleConfig.java ++++ FastQC/uk/ac/babraham/FastQC/Modules/ModuleConfig.java +@@ -23,6 +23,7 @@ import java.io.BufferedReader; + import java.io.FileNotFoundException; + import java.io.FileReader; + import java.io.InputStream; ++import java.io.FileInputStream; + import java.io.InputStreamReader; + import java.util.HashMap; + +@@ -82,7 +83,8 @@ public class ModuleConfig { + + try { + if (FastQCConfig.getInstance().limits_file == null) { +- InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/limits.txt"); ++ //InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/limits.txt"); ++ InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/limits.txt"); + if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/limits.txt"); + br =new BufferedReader(new InputStreamReader(rsrc)); + } +Index: FastQC/uk/ac/babraham/FastQC/Modules/AdapterContent.java +=================================================================== +--- FastQC.orig/uk/ac/babraham/FastQC/Modules/AdapterContent.java ++++ FastQC/uk/ac/babraham/FastQC/Modules/AdapterContent.java +@@ -27,6 +27,7 @@ import java.io.FileNotFoundException; + import java.io.FileReader; + import java.io.IOException; + import java.io.InputStream; ++import java.io.FileInputStream; + import java.io.InputStreamReader; + import java.util.Vector; + import java.util.zip.ZipEntry; +@@ -75,8 +76,9 @@ public class AdapterContent extends Abst + + BufferedReader br = null; + if (FastQCConfig.getInstance().adapter_file == null) { +- InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/adapter_list.txt"); +- if (rsrc==null) throw new FileNotFoundException("cannot find Confituration/adapter_list.txt"); ++ //InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/usr/share/fastqc/Configuration/adapter_list.txt"); ++ InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/adapter_list.txt"); ++ if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/adapter_list.txt"); + br =new BufferedReader(new InputStreamReader(rsrc)); + } + else { +Index: FastQC/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java +=================================================================== +--- FastQC.orig/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java ++++ FastQC/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java +@@ -24,6 +24,7 @@ import java.io.FileNotFoundException; + import java.io.FileReader; + import java.io.IOException; + import java.io.InputStream; ++import java.io.FileInputStream; + import java.io.InputStreamReader; + import java.util.Vector; + +@@ -65,8 +66,9 @@ public class ContaminentFinder { + + BufferedReader br = null; + if (FastQCConfig.getInstance().contaminant_file == null) { +- InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/contaminant_list.txt"); +- if (rsrc==null) throw new FileNotFoundException("cannot find Confituration/contaminant_list.txt"); ++ //InputStream rsrc=ContaminentFinder.class.getResourceAsStream("/Configuration/contaminant_list.txt"); ++ InputStream rsrc = new FileInputStream("/etc/fastqc/Configuration/contaminant_list.txt"); ++ if (rsrc==null) throw new FileNotFoundException("cannot find Configuration/contaminant_list.txt"); + br =new BufferedReader(new InputStreamReader(rsrc)); + } + else { _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
