[med-svn] r21695 - in trunk/packages/logol/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Tue Apr 12 09:14:26 UTC 2016
Author: osallou
Date: 2016-04-12 09:14:25 +0000 (Tue, 12 Apr 2016)
New Revision: 21695
Modified:
trunk/packages/logol/trunk/debian/changelog
trunk/packages/logol/trunk/debian/get-orig-source.sh
trunk/packages/logol/trunk/debian/patches/remove_drmaa_support
trunk/packages/logol/trunk/debian/patches/remove_rubygems_usage
trunk/packages/logol/trunk/debian/patches/series
trunk/packages/logol/trunk/debian/patches/setDebianDirs
trunk/packages/logol/trunk/debian/watch
Log:
prepare new upstream release 1.7.4
Modified: trunk/packages/logol/trunk/debian/changelog
===================================================================
--- trunk/packages/logol/trunk/debian/changelog 2016-04-12 08:57:23 UTC (rev 21694)
+++ trunk/packages/logol/trunk/debian/changelog 2016-04-12 09:14:25 UTC (rev 21695)
@@ -1,3 +1,9 @@
+logol (1.7.4-1) UNRELEASED; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 12 Apr 2016 10:51:02 +0200
+
logol (1.7.2-3) unstable; urgency=medium
* Team upload.
Modified: trunk/packages/logol/trunk/debian/get-orig-source.sh
===================================================================
--- trunk/packages/logol/trunk/debian/get-orig-source.sh 2016-04-12 08:57:23 UTC (rev 21694)
+++ trunk/packages/logol/trunk/debian/get-orig-source.sh 2016-04-12 09:14:25 UTC (rev 21695)
@@ -3,20 +3,20 @@
set -e
PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --rename --verbose --force-download |
- grep "Newest version on remote site is .* local version is .*" |
- head -n 1 |
- sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
-
-#VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }'| cut -d"-" -f1`
+#VERSION=`uscan --rename --verbose --force-download |
+# grep "Newest version on remote site is .* local version is .*" |
+# head -n 1 |
+# sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+uscan --rename --verbose --force-download
+VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }'| cut -d"-" -f1`
#svn export svn://scm.gforge.inria.fr/svn/logolexec/trunk/LogolExec ${PKG}-${VERSION}.orig
mkdir -p ../tarballs
cd ../tarballs
-UTAR="${PKG}_${VERSION}.orig.tar.xz"
+UTAR="${PKG}_${VERSION}.orig.tar.gz"
mv ../${UTAR} .
-tar xfJ ${UTAR}
+tar xfz ${UTAR}
mv ${PKG}-${VERSION} ${PKG}-${VERSION}.orig
Modified: trunk/packages/logol/trunk/debian/patches/remove_drmaa_support
===================================================================
--- trunk/packages/logol/trunk/debian/patches/remove_drmaa_support 2016-04-12 08:57:23 UTC (rev 21694)
+++ trunk/packages/logol/trunk/debian/patches/remove_drmaa_support 2016-04-12 09:14:25 UTC (rev 21695)
@@ -9,8 +9,8 @@
--- a/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
+++ b/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
@@ -230,7 +230,6 @@
- options.addOption("h",false,"get usage");
-
+ options.addOption("h",false,"get usage");
+
options.addOption("s", true, "sequence database");
- options.addOption("sge", false, "use SGE");
options.addOption("local", false, "use local system");
@@ -33,8 +33,8 @@
- type=SGE;
- jobmngr = (JobManager) new SGEJobManager();
- }
- if( cmd.hasOption( "dna" ) ) {
- format=1;
+ if( cmd.hasOption( "dna" ) ) {
+ format=1;
}
--- a/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
+++ b/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
Modified: trunk/packages/logol/trunk/debian/patches/remove_rubygems_usage
===================================================================
--- trunk/packages/logol/trunk/debian/patches/remove_rubygems_usage 2016-04-12 08:57:23 UTC (rev 21694)
+++ trunk/packages/logol/trunk/debian/patches/remove_rubygems_usage 2016-04-12 09:14:25 UTC (rev 21695)
@@ -15,14 +15,14 @@
--- a/tools/logolSearch.rb
+++ b/tools/logolSearch.rb
@@ -22,9 +22,9 @@
- DIR=File.expand_path(File.dirname(__FILE__))
-
- if muteOnly.to_i == 1
-- cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming"
-+ cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming"
- else
-- cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError
-+ cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError
- end
-
- Open3.popen3(cmd) do |stdin,stdout,stderr, wait_thr|
+ DIR=File.expand_path(File.dirname(__FILE__))
+
+ if muteOnly.to_i == 1
+- cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming"
++ cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming"
+ else
+- cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError
++ cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError
+ end
+
+ Open3.popen3(cmd) do |stdin,stdout,stderr, wait_thr|
Modified: trunk/packages/logol/trunk/debian/patches/series
===================================================================
--- trunk/packages/logol/trunk/debian/patches/series 2016-04-12 08:57:23 UTC (rev 21694)
+++ trunk/packages/logol/trunk/debian/patches/series 2016-04-12 09:14:25 UTC (rev 21695)
@@ -4,5 +4,5 @@
setDebianDirs
fix_doc_generation
remove_rubygems_usage
-fix_swipl72
+#fix_swipl72
fix_antlr35
Modified: trunk/packages/logol/trunk/debian/patches/setDebianDirs
===================================================================
--- trunk/packages/logol/trunk/debian/patches/setDebianDirs 2016-04-12 08:57:23 UTC (rev 21694)
+++ trunk/packages/logol/trunk/debian/patches/setDebianDirs 2016-04-12 09:14:25 UTC (rev 21695)
@@ -2,18 +2,6 @@
Description: Debian policy hierarchy use
Author: Olivier Sallou <osallou at debian.org>
Last-Updated: 2012-06-18
---- a/log4j.properties
-+++ b/log4j.properties
-@@ -13,6 +13,6 @@
-
-
- log4j.appender.A2=org.apache.log4j.FileAppender
--log4j.appender.A2.File=/home/osallou/CODE/TEST/logol.log
-+log4j.appender.A2.File=/var/log/logol/logol.log
- log4j.appender.A2.layout=org.apache.log4j.PatternLayout
--log4j.appender.A2.layout.ConversionPattern=%d{MM-dd at HH:mm:ss} %-5p (%13F:%L) %3x - %m%n
-\ No newline at end of file
-+log4j.appender.A2.layout.ConversionPattern=%d{MM-dd at HH:mm:ss} %-5p (%13F:%L) %3x - %m%n
--- a/prolog/logol.properties
+++ b/prolog/logol.properties
@@ -11,9 +11,9 @@
@@ -41,7 +29,7 @@
JAVA_OPTS=" -Xms512m -Xmx4096m"
fi
--java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar org.irisa.genouest.logol.Logol $*
+-java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar org.irisa.genouest.logol.Logol $*
+java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar org.irisa.genouest.logol.Logol $*
--- a/LogolMultiExec.sh
@@ -50,6 +38,16 @@
echo "calling logol with parameters "$*
--java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar org.irisa.genouest.logol.dispatcher.Dispatch $*
+-java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar org.irisa.genouest.logol.dispatcher.Dispatch $*
+java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar org.irisa.genouest.logol.dispatcher.Dispatch $*
+--- a/log4j.properties
++++ b/log4j.properties
+@@ -13,6 +13,6 @@
+
+
+ log4j.appender.A2=org.apache.log4j.FileAppender
+-log4j.appender.A2.File=/tmp/logol.log
++log4j.appender.A2.File=/var/log/logol/logol.log
+ log4j.appender.A2.layout=org.apache.log4j.PatternLayout
+ log4j.appender.A2.layout.ConversionPattern=%d{MM-dd at HH:mm:ss} %-5p (%13F:%L) %3x - %m%n
Modified: trunk/packages/logol/trunk/debian/watch
===================================================================
--- trunk/packages/logol/trunk/debian/watch 2016-04-12 08:57:23 UTC (rev 21694)
+++ trunk/packages/logol/trunk/debian/watch 2016-04-12 09:14:25 UTC (rev 21695)
@@ -1,2 +1,4 @@
version=3
-https://gforge.inria.fr/frs/?group_id=1318 .*/logol_(\d[\d.-]+)\.orig\.tar\.bz2
+#https://gforge.inria.fr/frs/?group_id=1318 .*/logol_(\d[\d.-]+)\.orig\.tar\.bz2
+opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/logol-$1\.tar\.gz/ \
+ https://github.com/genouest/logol/tags .*/v?(\d\S*)\.tar\.gz
More information about the debian-med-commit
mailing list