[med-svn] r17795 - in trunk/packages/babraham/fastqc/tags: . 0.11.2+dfsg-2/debian 0.11.2+dfsg-2/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Tue Aug 19 10:40:37 UTC 2014
Author: osallou
Date: 2014-08-19 10:40:37 +0000 (Tue, 19 Aug 2014)
New Revision: 17795
Added:
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/README.Debian
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/changelog
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/Makefile.patch
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/series
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/set_configuration_path
Removed:
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/README.Debian
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/changelog
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/Makefile.patch
trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/series
Log:
[svn-buildpackage] Tagging fastqc 0.11.2+dfsg-2
Deleted: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/README.Debian
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/README.Debian 2014-08-19 06:53:11 UTC (rev 17782)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/README.Debian 2014-08-19 10:40:37 UTC (rev 17795)
@@ -1,79 +0,0 @@
-fastqc for Debian
------------------
-
-You can run FastQC in one of two modes, either as an interactive graphical application
-in which you can dynamically load FastQ files and view their results.
-
-Alternatively you can run FastQC in a non-interactive mode where you specify the files
-you want to process on the command line and FastQC will generate an HTML report for
-each file without launching a user interface. This would allow FastQC to be run as
-part of an analysis pipeline.
-
-
-Running FastQC Interactively
-----------------------------
-
-A wrapper is installed into /usr/bin/fastqc
-
-
-
-Running FastQC as part of a pipeline
-------------------------------------
-To run FastQC non-interactively you should use the fastqc wrapper script to launch
-the program.
-
-To run non-interactively you simply have to specify a list of files to process
-on the commandline
-
-fastqc somefile.txt someotherfile.txt
-
-You can specify as many files to process in a single run as you like. If you don't
-specify any files to process the program will try to open the interactive application
-which may result in an error if you're running in a non-graphical environment.
-
-There are a few extra options you can specify when running non-interactively. Full
-details of these can be found by running
-
-fastqc --help
-
-By default, in non-interactive mode FastQC will create both a zipped copy of the
-QC report, and also extract this to create a folder which contains the report
-files ready to be viewed. If you only want to create the zipped file then you can
-add
-
---noextract
-
-To the launch command to suppress the unzipping.
-
-If you want to save your reports in a folder other than the folder which contained
-your original FastQ files then you can specify an alternative location by setting a
---outdir value:
-
---outdir=/some/other/dir/
-
-Customising the report output
------------------------------
-
-If you want to run FastQC as part of a sequencing pipeline you may wish to change the
-formatting of the report to add in your own branding or to include extra information.
-
-In the Templates directory you will find a file called 'header_template.html' which
-you can edit to change the look of the report. This file contains all of the header for
-the report file, including the CSS section and you can alter this however you see fit.
-
-If you want to add in your own logo or other image files to the reports then you can drop
-a png or jpg file into the Icons folder in the templates directory and this will be copied
-into the report folder for all reports generated by the program. You can refer to these
-icons using a relative URL (eg Icons/image.png) in the HTML template. Images placed
-outside the icons directory will not be copied.
-
-Whilst you can make whatever changes you like you should probably leave in place the
-<div> structure of the html template since later code will expect to close the main div
-which is left open at the end of the header. There is no facility to change the code in
-the main body of the report or the footer (although you can of course change the styling).
-
-The text tags @@FILENAME@@ and @@DATE@@ are placeholders which are filled in when the
-report it created. You can use these placeholders in other parts of the header if you
-wish.
-
- -- Andreas Tille <tille at debian.org> Wed, 07 Nov 2012 14:24:25 +0100
Copied: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/README.Debian (from rev 17793, trunk/packages/babraham/fastqc/trunk/debian/README.Debian)
===================================================================
--- trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/README.Debian (rev 0)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/README.Debian 2014-08-19 10:40:37 UTC (rev 17795)
@@ -0,0 +1,84 @@
+fastqc for Debian
+-----------------
+
+You can run FastQC in one of two modes, either as an interactive graphical application
+in which you can dynamically load FastQ files and view their results.
+
+Alternatively you can run FastQC in a non-interactive mode where you specify the files
+you want to process on the command line and FastQC will generate an HTML report for
+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
+----------------------------
+
+A wrapper is installed into /usr/bin/fastqc
+
+
+
+Running FastQC as part of a pipeline
+------------------------------------
+To run FastQC non-interactively you should use the fastqc wrapper script to launch
+the program.
+
+To run non-interactively you simply have to specify a list of files to process
+on the commandline
+
+fastqc somefile.txt someotherfile.txt
+
+You can specify as many files to process in a single run as you like. If you don't
+specify any files to process the program will try to open the interactive application
+which may result in an error if you're running in a non-graphical environment.
+
+There are a few extra options you can specify when running non-interactively. Full
+details of these can be found by running
+
+fastqc --help
+
+By default, in non-interactive mode FastQC will create both a zipped copy of the
+QC report, and also extract this to create a folder which contains the report
+files ready to be viewed. If you only want to create the zipped file then you can
+add
+
+--noextract
+
+To the launch command to suppress the unzipping.
+
+If you want to save your reports in a folder other than the folder which contained
+your original FastQ files then you can specify an alternative location by setting a
+--outdir value:
+
+--outdir=/some/other/dir/
+
+Customising the report output
+-----------------------------
+
+If you want to run FastQC as part of a sequencing pipeline you may wish to change the
+formatting of the report to add in your own branding or to include extra information.
+
+In the Templates directory you will find a file called 'header_template.html' which
+you can edit to change the look of the report. This file contains all of the header for
+the report file, including the CSS section and you can alter this however you see fit.
+
+If you want to add in your own logo or other image files to the reports then you can drop
+a png or jpg file into the Icons folder in the templates directory and this will be copied
+into the report folder for all reports generated by the program. You can refer to these
+icons using a relative URL (eg Icons/image.png) in the HTML template. Images placed
+outside the icons directory will not be copied.
+
+Whilst you can make whatever changes you like you should probably leave in place the
+<div> structure of the html template since later code will expect to close the main div
+which is left open at the end of the header. There is no facility to change the code in
+the main body of the report or the footer (although you can of course change the styling).
+
+The text tags @@FILENAME@@ and @@DATE@@ are placeholders which are filled in when the
+report it created. You can use these placeholders in other parts of the header if you
+wish.
+
+ -- Andreas Tille <tille at debian.org> Wed, 07 Nov 2012 14:24:25 +0100
Deleted: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/changelog
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/changelog 2014-08-19 06:53:11 UTC (rev 17782)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/changelog 2014-08-19 10:40:37 UTC (rev 17795)
@@ -1,18 +0,0 @@
-fastqc (0.11.2+dfsg-1) unstable; urgency=medium
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> Mon, 09 Jun 2014 10:41:06 +0200
-
-fastqc (0.10.1+dfsg-2) unstable; urgency=low
-
- * Add patch to fix Templates and Contaminants loading
- in non interactive mode (Closes: #697604)
-
- -- Olivier Sallou <osallou at debian.org> Wed, 05 Jun 2013 17:08:44 +0200
-
-fastqc (0.10.1+dfsg-1) unstable; urgency=low
-
- * Initial release (Closes: #670353)
-
- -- Andreas Tille <tille at debian.org> Tue, 20 Nov 2012 13:38:32 +0100
Copied: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/changelog (from rev 17794, trunk/packages/babraham/fastqc/trunk/debian/changelog)
===================================================================
--- trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/changelog (rev 0)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/changelog 2014-08-19 10:40:37 UTC (rev 17795)
@@ -0,0 +1,25 @@
+fastqc (0.11.2+dfsg-2) unstable; 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
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 09 Jun 2014 10:41:06 +0200
+
+fastqc (0.10.1+dfsg-2) unstable; urgency=low
+
+ * Add patch to fix Templates and Contaminants loading
+ in non interactive mode (Closes: #697604)
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 05 Jun 2013 17:08:44 +0200
+
+fastqc (0.10.1+dfsg-1) unstable; urgency=low
+
+ * Initial release (Closes: #670353)
+
+ -- Andreas Tille <tille at debian.org> Tue, 20 Nov 2012 13:38:32 +0100
Deleted: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch 2014-08-19 06:53:11 UTC (rev 17782)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/Makefile.patch 2014-08-19 10:40:37 UTC (rev 17795)
@@ -1,27 +0,0 @@
-From: Steffen Moeller <moeller at debian.org>
-Subject: Simplyfy installation by creating a Makefile
-
---- /dev/null
-+++ b/Makefile
-@@ -0,0 +1,19 @@
-+
-+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"`
-+
-+DESTDIR=
-+PREFIX=/usr
-+install: fastqc.jar
-+ mkdir -p $(DESTDIR)$(PREFIX)/bin/
-+ cp -a fastqc $(DESTDIR)$(PREFIX)/bin/
-+ 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/
-+
-+clean:
-+ find . -name "*.jar" -o -name "*.class" | xargs -r rm
-+
-+.PHONY: all install
Copied: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/Makefile.patch (from rev 17793, trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch)
===================================================================
--- trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/Makefile.patch (rev 0)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/Makefile.patch 2014-08-19 10:40:37 UTC (rev 17795)
@@ -0,0 +1,29 @@
+From: Steffen Moeller <moeller at debian.org>
+Subject: Simplyfy installation by creating a Makefile
+
+Index: FastQC/Makefile
+===================================================================
+--- /dev/null
++++ 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"` `find net -name "*.class" -o -name "*.png"` Templates
++
++DESTDIR=
++PREFIX=/usr
++install: fastqc.jar
++ mkdir -p $(DESTDIR)$(PREFIX)/bin/
++ cp -a fastqc $(DESTDIR)$(PREFIX)/bin/
++ chmod +x $(DESTDIR)$(PREFIX)/bin/fastqc
++ mkdir -p $(DESTDIR)$(PREFIX)/share/fastqc/
++ cp -a fastqc.jar $(DESTDIR)$(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
Deleted: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/series
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/series 2014-08-19 06:53:11 UTC (rev 17782)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/series 2014-08-19 10:40:37 UTC (rev 17795)
@@ -1,3 +0,0 @@
-Makefile.patch
-fastqc.patch
-fix-help-call.patch
Copied: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/series (from rev 17793, trunk/packages/babraham/fastqc/trunk/debian/patches/series)
===================================================================
--- trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/series (rev 0)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/series 2014-08-19 10:40:37 UTC (rev 17795)
@@ -0,0 +1,4 @@
+Makefile.patch
+fastqc.patch
+fix-help-call.patch
+set_configuration_path
Copied: trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/set_configuration_path (from rev 17794, trunk/packages/babraham/fastqc/trunk/debian/patches/set_configuration_path)
===================================================================
--- trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/set_configuration_path (rev 0)
+++ trunk/packages/babraham/fastqc/tags/0.11.2+dfsg-2/debian/patches/set_configuration_path 2014-08-19 10:40:37 UTC (rev 17795)
@@ -0,0 +1,75 @@
+Subject: load config in /etc
+Description: use config in Debian etc dirs instead of embedding data in jar
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2014-08-19
+Forwarded: no
+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