[med-svn] [varscan] 05/06: cme fix dpkg-control; update changelog; really drop unused quilt patch
Andreas Tille
tille at debian.org
Wed Jul 8 03:25:50 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository varscan.
commit c8838c6ed063f6c6c6abfb564816abf08da43646
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 8 05:17:17 2015 +0200
cme fix dpkg-control; update changelog; really drop unused quilt patch
---
debian/changelog | 2 +
debian/control | 11 ++--
debian/patches/series | 1 -
debian/patches/usage.patch | 159 ---------------------------------------------
4 files changed, 8 insertions(+), 165 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 2db5e96..725c547 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,8 @@
varscan (2.3.9+dfsg-1) UNRELEASED; urgency=medium
* New upstream version
+ * Do not use patches to fix usage any more but fix it using sed in debian/rules
+ * cme fix dpkg-control
-- Andreas Tille <tille at debian.org> Wed, 08 Jul 2015 04:54:26 +0200
diff --git a/debian/control b/debian/control
index 9d0427e..71ec949 100644
--- a/debian/control
+++ b/debian/control
@@ -1,14 +1,15 @@
Source: varscan
-Section: non-free/science
-Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
+Section: non-free/science
+XS-Autobuild: no
+Priority: optional
Build-Depends: debhelper (>= 9),
- javahelper (>=0.25),
+ javahelper,
default-jdk,
ant
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/varscan.git
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/varscan.git
Vcs-Git: git://anonscm.debian.org/debian-med/varscan.git
Homepage: http://varscan.sourceforge.net/
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 3060795..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1 +0,0 @@
-# usage.patch
diff --git a/debian/patches/usage.patch b/debian/patches/usage.patch
deleted file mode 100644
index 1777246..0000000
--- a/debian/patches/usage.patch
+++ /dev/null
@@ -1,159 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Updated: Tue, 15 Apr 2014 13:38:37 +0200
-Forwarded: no
-Description: Adapt usage message to Debian installation
-
---- a/net/sf/varscan/CallMpileup.java
-+++ b/net/sf/varscan/CallMpileup.java
-@@ -28,7 +28,7 @@ public class CallMpileup {
- public CallMpileup(String[] args, String callType)
- {
- // Define the usage message //
-- String usage = "USAGE: java -jar VarScan.jar mpileup2cns [pileup file] OPTIONS\n" +
-+ String usage = "USAGE: varscan mpileup2cns [pileup file] OPTIONS\n" +
- "\tmpileup file - The SAMtools mpileup file\n" +
- "\n" +
- "\tOPTIONS:\n" +
---- a/net/sf/varscan/CallPileup.java
-+++ b/net/sf/varscan/CallPileup.java
-@@ -24,7 +24,7 @@ public class CallPileup {
- public CallPileup(String[] args, String callType)
- {
- // Define the usage message //
-- String usage = "USAGE: java -jar VarScan.jar pileup2cns [pileup file] OPTIONS\n" +
-+ String usage = "USAGE: varscan pileup2cns [pileup file] OPTIONS\n" +
- "\tpileup file - The SAMtools pileup file\n" +
- "\n" +
- "\tOPTIONS:\n" +
---- a/net/sf/varscan/Comparison.java
-+++ b/net/sf/varscan/Comparison.java
-@@ -27,7 +27,7 @@ public class Comparison {
-
- public Comparison(String[] args)
- {
-- String usage = "USAGE: java -jar VarScan.jar compare [file1] [file2] [type] [output] OPTIONS\n" +
-+ String usage = "USAGE: varscan compare [file1] [file2] [type] [output] OPTIONS\n" +
- "\tfile1 - A file of chromosome-positions, tab-delimited\n" +
- "\tfile2 - A file of chromosome-positions, tab-delimited\n" +
- "\ttype - Type of comparison [intersect|merge|unique1|unique2]\n" +
---- a/net/sf/varscan/CopyCaller.java
-+++ b/net/sf/varscan/CopyCaller.java
-@@ -28,7 +28,7 @@ import java.util.HashMap;
- public class CopyCaller {
- public CopyCaller(String[] args, HashMap<String, String> params)
- {
-- String usage = "USAGE: java -jar VarScan.jar copyCaller [varScan.copynumber] OPTIONS\n" +
-+ String usage = "USAGE: varscan copyCaller [varScan.copynumber] OPTIONS\n" +
- "This command will adjust VarScan copynumber output for GC content, apply amp/del thresholds,\n and (optionally) recenter the data\n" +
- "\tINPUT:\n" +
- "\tRaw output from the VarScan copynumber command (eg. varScan.output.copynumber)\n\n" +
---- a/net/sf/varscan/Copynumber.java
-+++ b/net/sf/varscan/Copynumber.java
-@@ -22,7 +22,7 @@ public class Copynumber {
- ////////////////////////////////////////////////////////////////////////////////////////////////////
- public Copynumber(String[] args, boolean isMpileup)
- {
-- String usage = "USAGE: java -jar VarScan.jar copynumber [normal-tumor.mpileup] [Opt: output] OPTIONS\n" +
-+ String usage = "USAGE: varscan copynumber [normal-tumor.mpileup] [Opt: output] OPTIONS\n" +
- "\tnormal-tumor.mpileup - The SAMtools mpileup file for Normal and Tumor\n" +
- "\toutput - Output base name for files\n" +
- "\nOPTIONS:\n" +
---- a/net/sf/varscan/Coverage.java
-+++ b/net/sf/varscan/Coverage.java
-@@ -29,7 +29,7 @@ public class Coverage {
- public Coverage(String[] args)
- {
- // Define the usage message //
-- String usage = "USAGE: java -jar VarScan.jar coverage [pileup-file] OPTIONS\n" +
-+ String usage = "USAGE: varscan coverage [pileup-file] OPTIONS\n" +
- "\n" +
- "\tpileup-file - A SAMtools pileup file or piped input\n" +
- "\tOPTIONS:\n" +
---- a/net/sf/varscan/FilterSomatic.java
-+++ b/net/sf/varscan/FilterSomatic.java
-@@ -29,7 +29,7 @@ public class FilterSomatic {
- public FilterSomatic(String[] args)
- {
- // Define the usage message //
-- String usage = "USAGE: java -jar VarScan.jar filter [variant file] OPTIONS\n" +
-+ String usage = "USAGE: varscan filter [variant file] OPTIONS\n" +
- "\tvariant file - A file of SNPs or indels\n" +
- "\n" +
- "\tOPTIONS:\n" +
---- a/net/sf/varscan/FilterVariants.java
-+++ b/net/sf/varscan/FilterVariants.java
-@@ -28,7 +28,7 @@ public class FilterVariants {
- public FilterVariants(String[] args)
- {
- // Define the usage message //
-- String usage = "USAGE: java -jar VarScan.jar filter [variant file] OPTIONS\n" +
-+ String usage = "USAGE: varscan filter [variant file] OPTIONS\n" +
- "\tvariant file - A file of SNPs or indels\n" +
- "\n" +
- "\tOPTIONS:\n" +
---- a/net/sf/varscan/LimitVariants.java
-+++ b/net/sf/varscan/LimitVariants.java
-@@ -27,7 +27,7 @@ public class LimitVariants {
-
- public LimitVariants(String[] args)
- {
-- String usage = "USAGE: java -jar VarScan.jar limit [infile] OPTIONS\n" +
-+ String usage = "USAGE: varscan limit [infile] OPTIONS\n" +
- "\tinfile - A file of chromosome-positions, tab-delimited\n" +
- "\tOPTIONS\n" +
- "\t--positions-file - a file of chromosome-positions, tab delimited, or VCF\n" +
---- a/net/sf/varscan/ProcessSomatic.java
-+++ b/net/sf/varscan/ProcessSomatic.java
-@@ -19,7 +19,7 @@ public class ProcessSomatic {
-
- public ProcessSomatic(String[] args)
- {
-- String usage = "USAGE: java -jar VarScan.jar process [status-file] OPTIONS\n" +
-+ String usage = "USAGE: varscan process [status-file] OPTIONS\n" +
- "\tstatus-file - The VarScan output file for SNPs or Indels\n" +
- "\tOPTIONS\n" +
- "\t--min-tumor-freq - Minimum variant allele frequency in tumor [0.10]\n" +
---- a/net/sf/varscan/ReadCounts.java
-+++ b/net/sf/varscan/ReadCounts.java
-@@ -28,7 +28,7 @@ public class ReadCounts {
-
- public ReadCounts(String[] args, HashMap<String, String> params)
- {
-- String usage = "USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS\n" +
-+ String usage = "USAGE: varscan readcounts [pileup] OPTIONS\n" +
- "\tOPTIONS:\n" +
- "\t--variants-file\tA list of variants at which to report readcounts\n" +
- "\t--output-file\tOutput file to contain the readcounts\n" +
---- a/net/sf/varscan/Somatic.java
-+++ b/net/sf/varscan/Somatic.java
-@@ -34,7 +34,7 @@ public class Somatic {
-
- public Somatic(String[] args, boolean isMpileup)
- {
-- String usage = "USAGE: java -jar VarScan.jar somatic [normal-tumor.mpileup] [Opt: output] OPTIONS\n" +
-+ String usage = "USAGE: varscan somatic [normal-tumor.mpileup] [Opt: output] OPTIONS\n" +
- "\tnormal-tumor.pileup - The SAMtools mpileup file for Normal and Tumor BAMs\n" +
- "\toutput - Output base name for SNP and indel output\n" +
- "\nOPTIONS:\n" +
---- a/net/sf/varscan/Trio.java
-+++ b/net/sf/varscan/Trio.java
-@@ -29,7 +29,7 @@ public class Trio {
- public Trio(String[] args, String callType)
- {
- // Define the usage message //
-- String usage = "USAGE: java -jar VarScan.jar trio [mpileup file] [output-basename] OPTIONS\n" +
-+ String usage = "USAGE: varscan trio [mpileup file] [output-basename] OPTIONS\n" +
- "\tmpileup file - The SAMtools mpileup file for father, mother, child in that order\n" +
- "\n" +
- "\tOPTIONS:\n" +
---- a/net/sf/varscan/VarScan.java
-+++ b/net/sf/varscan/VarScan.java
-@@ -105,7 +105,7 @@ public class VarScan {
- */
- public static void main(String[] args) {
-
-- String usage = "VarScan v2.3\n\nUSAGE: java -jar VarScan.jar [COMMAND] [OPTIONS] \n\n";
-+ String usage = "VarScan v2.3\n\nUSAGE: varscan [COMMAND] [OPTIONS] \n\n";
- usage = usage + "COMMANDS:\n" +
- "\tpileup2snp\t\tIdentify SNPs from a pileup file\n" +
- "\tpileup2indel\t\tIdentify indels a pileup file\n" +
--
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