[med-svn] r17793 - in trunk/packages/babraham/fastqc/trunk/debian: . patches

Olivier Sallou osallou at moszumanska.debian.org
Tue Aug 19 10:32:57 UTC 2014 

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 <osallou at debian.org>  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 <moeller at debian.org>
 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 {

More information about the debian-med-commit mailing list