# HG changeset patch # User timpalpant # Date 1329634468 18000 # Node ID 4fc118372ae75362e9a3236ce165fa217cf3c56f # Parent 422ac2bbb274a750a8a319d91249e1fb16728181 Uploaded new version with fixes and broader support for interval files diff -r 422ac2bbb274 -r 4fc118372ae7 dist/java-genomics-toolkit.jar Binary file dist/java-genomics-toolkit.jar has changed diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/._BaseAlignCounts.xml Binary file galaxy-conf/._BaseAlignCounts.xml has changed diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/._Phasogram.xml Binary file galaxy-conf/._Phasogram.xml has changed diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/BaseAlignCounts.xml --- a/galaxy-conf/BaseAlignCounts.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/BaseAlignCounts.xml Sun Feb 19 01:54:28 2012 -0500 @@ -2,8 +2,8 @@ of sequencing reads galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output - - + + diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/MapDyads.xml --- a/galaxy-conf/MapDyads.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/MapDyads.xml Sun Feb 19 01:54:28 2012 -0500 @@ -7,7 +7,7 @@ #end if - + diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/Phasogram.xml --- a/galaxy-conf/Phasogram.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/Phasogram.xml Sun Feb 19 01:54:28 2012 -0500 @@ -2,7 +2,7 @@ of dyads galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output - + diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/RollingReadLength.xml --- a/galaxy-conf/RollingReadLength.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/RollingReadLength.xml Sun Feb 19 01:54:28 2012 -0500 @@ -2,7 +2,7 @@ from paired-end sequencing reads galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output - + diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/WigSummary.xml --- a/galaxy-conf/WigSummary.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/WigSummary.xml Sun Feb 19 01:54:28 2012 -0500 @@ -5,7 +5,7 @@ - + diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/log4j.properties --- a/galaxy-conf/log4j.properties Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/log4j.properties Sun Feb 19 01:54:28 2012 -0500 @@ -1,10 +1,10 @@ -log4j.rootLogger=warn, stdout +log4j.rootLogger=info, stdout log4j.appender.stdout=org.apache.log4j.ConsoleAppender log4j.appender.stdout.layout=org.apache.log4j.PatternLayout # Pattern to output the caller's file name and line number. -log4j.appender.stdout.layout.ConversionPattern=%5p - %m%n +log4j.appender.stdout.layout.ConversionPattern=%m%n # Only output errors from the BigWig library log4j.logger.org.broad.igv.bbfile=ERROR \ No newline at end of file diff -r 422ac2bbb274 -r 4fc118372ae7 lib/.DS_Store Binary file lib/.DS_Store has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/._.DS_Store Binary file lib/._.DS_Store has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/._bin Binary file lib/._bin has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/._macify-1.4.jar Binary file lib/._macify-1.4.jar has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._COPYING Binary file lib/bin/._COPYING has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._ld Binary file lib/bin/._ld has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._readme.txt Binary file lib/bin/._readme.txt has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._windres Binary file lib/bin/._windres has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/COPYING --- a/lib/bin/COPYING Tue Feb 14 18:40:50 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,340 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc. - 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. 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If this is what you want to do, use the GNU Library General -Public License instead of this License. diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/ld Binary file lib/bin/ld has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/readme.txt --- a/lib/bin/readme.txt Tue Feb 14 18:40:50 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -The MinGW binutils were built on Mac OS X 10.4 by Peter Centgraf diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/windres Binary file lib/bin/windres has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/java-genomics-io.jar Binary file lib/java-genomics-io.jar has changed diff -r 422ac2bbb274 -r 4fc118372ae7 lib/mg4j-2.0.1.jar Binary file lib/mg4j-2.0.1.jar has changed