This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository canu.
commit e9a8c24a67cdf0b70dd0ed638d07f30b813fb0de Author: Afif Elghraoui <[email protected]> Date: Mon Mar 20 22:47:18 2017 -0400 Refresh patches --- debian/patches/external-deps.patch | 2 +- debian/patches/use-debian-mhap-at-runtime.patch | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/debian/patches/external-deps.patch b/debian/patches/external-deps.patch index 7965606..516daf8 100644 --- a/debian/patches/external-deps.patch +++ b/debian/patches/external-deps.patch @@ -3,7 +3,7 @@ Author: Afif Elghraoui <[email protected]> Forwarded: not-needed --- canu.orig/src/main.mk +++ canu/src/main.mk -@@ -145,7 +145,6 @@ +@@ -157,7 +157,6 @@ \ overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.mk \ \ diff --git a/debian/patches/use-debian-mhap-at-runtime.patch b/debian/patches/use-debian-mhap-at-runtime.patch index 108e459..f71079a 100644 --- a/debian/patches/use-debian-mhap-at-runtime.patch +++ b/debian/patches/use-debian-mhap-at-runtime.patch @@ -4,21 +4,21 @@ Forwarded: not-needed Last-Update: 2016-03-20 --- canu.orig/src/pipelines/canu/OverlapMhap.pm +++ canu/src/pipelines/canu/OverlapMhap.pm -@@ -357,7 +357,7 @@ +@@ -350,7 +350,7 @@ print F "cd $path/blocks\n"; print F "\n"; - print F "$javaPath -d64 -server -Xmx", getGlobal("${tag}mhapMemory"), "g \\\n"; + print F "$javaPath -d64 -server -Xmx", $javaMemory, "m \\\n"; - print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "\$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; + print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "/usr/share/java/mhap.jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; - print F " --repeat-weight 0.9 -k $merSize \\\n"; + print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n"; print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1); print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1); -@@ -434,7 +434,7 @@ +@@ -421,7 +421,7 @@ print F "\n"; print F "if [ ! -e \"$path/results/\$qry.mhap\" ] ; then\n"; - print F " $javaPath -d64 -server -Xmx", getGlobal("${tag}mhapMemory"), "g \\\n"; + print F " $javaPath -d64 -server -Xmx", $javaMemory, "m \\\n"; - print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "\$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; + print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "/usr/share/java//mhap.jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; - print F " --repeat-weight 0.9 -k $merSize \\\n"; + print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n"; print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1); print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/canu.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
