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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 05 Jun 2013 17:08:44 +0200 - -fastqc (0.10.1+dfsg-1) unstable; urgency=low - - * Initial release (Closes: #670353) - - -- Andreas Tille <[email protected]> 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 <[email protected]> Tue, 19 Aug 2014 09:06:07 +0200 + +fastqc (0.11.2+dfsg-1) unstable; urgency=medium + + * New upstream release + + -- Olivier Sallou <[email protected]> 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 <[email protected]> Wed, 05 Jun 2013 17:08:44 +0200 + +fastqc (0.10.1+dfsg-1) unstable; urgency=low + + * Initial release (Closes: #670353) + + -- Andreas Tille <[email protected]> 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 <[email protected]> -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 <[email protected]> +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 <[email protected]> +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 { _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
