[med-svn] [trinityrnaseq] 04/04: update patches for 2.0.4
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 16 07:10:16 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit e512079b6969a13b33461b227c63682f952b6f57
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Mon Feb 16 01:09:53 2015 -0500
update patches for 2.0.4
---
debian/changelog | 2 +-
debian/patches/chrysalis-make-tweak | 24 ++-------------
debian/patches/jellyfish-path | 2 +-
debian/patches/noExitTester | 2 +-
debian/patches/update-paths | 59 ++-----------------------------------
debian/rules | 5 ++--
6 files changed, 11 insertions(+), 83 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index e3212aa..df7d6fc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-trinityrnaseq (2.0.3+dfsg-1) UNRELEASED; urgency=low
+trinityrnaseq (2.0.4+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #777697)
diff --git a/debian/patches/chrysalis-make-tweak b/debian/patches/chrysalis-make-tweak
index 526a8df..093c9ca 100644
--- a/debian/patches/chrysalis-make-tweak
+++ b/debian/patches/chrysalis-make-tweak
@@ -1,27 +1,9 @@
-Description: <short summary of the patch>
- TODO: Put a short summary on the line above and replace this paragraph
- with a longer explanation of this change. Complete the meta-information
- with other relevant fields (see below for details). To make it easier, the
- information below has been extracted from the changelog. Adjust it or drop
- it.
- .
- trinityrnaseq (2.0.2-1) UNRELEASED; urgency=low
- .
- * Initial release (Closes: #<bug>)
-Author: DMPT <debian-med-packaging at lists.alioth.debian.org>
+Description: don't die if a file is missing
+Author: Michael R. Crusoe <mcrusoe at msu.edu>
---
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
+Last-Update: 2015-02-16
--- trinityrnaseq.orig/Chrysalis/Makefile
+++ trinityrnaseq/Chrysalis/Makefile
diff --git a/debian/patches/jellyfish-path b/debian/patches/jellyfish-path
index 7e0d35e..aca6a33 100644
--- a/debian/patches/jellyfish-path
+++ b/debian/patches/jellyfish-path
@@ -1,7 +1,7 @@
Description:Jellyfish path
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -36,7 +36,7 @@
+@@ -38,7 +38,7 @@
my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
diff --git a/debian/patches/noExitTester b/debian/patches/noExitTester
index 084f783..0eaa9c8 100644
--- a/debian/patches/noExitTester
+++ b/debian/patches/noExitTester
@@ -1,7 +1,7 @@
Description:NoExitTester
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -2187,32 +2187,6 @@
+@@ -2191,32 +2191,6 @@
die "Error, cannot find 'java'. Please be sure it is available within your \${PATH} setting and then try again.";
}
diff --git a/debian/patches/update-paths b/debian/patches/update-paths
index 02ca370..9a6d461 100644
--- a/debian/patches/update-paths
+++ b/debian/patches/update-paths
@@ -1,41 +1,6 @@
---- trinityrnaseq.orig/util/support_scripts/trinity_install_tests.sh
-+++ trinityrnaseq/util/support_scripts/trinity_install_tests.sh
-@@ -6,14 +6,14 @@
- echo ' '
- echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-
--if [ -e "trinity-plugins/jellyfish/jellyfish" ]
-+if [ -e "/usr/bin/jellyfish" ]
- then
- echo "JellyFish: has been Installed Properly"
- else
- echo "JellyFish Installation appears to have FAILED"
- fi
-
--if [ -e "Inchworm/bin/inchworm" ]
-+if [ -e "debian/trinityrnaseq/usr/lib/trinityrnaseq/Inchworm/bin/inchworm" ]
- then
- echo "Inchworm: has been Installed Properly"
- else
-@@ -46,13 +46,13 @@
- echo "ReadsToTranscripts Installation appears to have FAILED"
- fi
-
--if [ -e "trinity-plugins/fastool/fastool" ]
-+if [ -e "debian/trinityrnaseq/usr/lib/trinityrnaseq/trinity-plugins/fastool/fastool" ]
- then
- echo "fastool: has been Installed Properly"
- else
- echo "fastool Installation appears to have FAILED"
- fi
--if [ -e "trinity-plugins/parafly/bin/ParaFly" ]
-+if [ -e "/usr/bin/ParaFly" ]
- then
- echo "parafly: has been Installed Properly"
- else
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -30,18 +30,18 @@
+@@ -32,18 +32,18 @@
open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
#directory defnintions
@@ -58,8 +23,8 @@
+my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
- #&version_check();
-@@ -319,7 +319,7 @@
+
+@@ -320,7 +320,7 @@
### Butterfly-related options: ####
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
@@ -79,21 +44,3 @@
commandArg<bool> skipCmmd("-skip","skip initial 2 steps", false);
commandArg<bool> strandCmmd("-strand","strand-specific data", false);
commandArg<bool> nobreakCmmd("-nobreak","skip breaking", false);
---- trinityrnaseq.orig/util/support_scripts/plugin_install_tests.sh
-+++ trinityrnaseq/util/support_scripts/plugin_install_tests.sh
-@@ -9,13 +9,13 @@
- else
- echo "slclust Installation appears to have FAILED"
- fi
--if [ -e "trinity-plugins/collectl/bin/collectl" ]
-+if [ -e "/usr/bin/collectl" ]
- then
- echo "collectl: has been Installed Properly"
- else
- echo "collectl Installation appears to have FAILED"
- fi
--if [ -e "trinity-plugins/rsem/rsem-calculate-expression" ]
-+if [ -e "/usr/bin/rsem-calculate-expression" ]
- then
- echo "rsem: has been Installed Properly"
- else
diff --git a/debian/rules b/debian/rules
index 5aee352..e7b6547 100755
--- a/debian/rules
+++ b/debian/rules
@@ -28,9 +28,8 @@ override_dh_auto_clean:
rm Chrysalis/Makefile_auto
override_dh_auto_test:
- java -jar Butterfly/Butterfly.jar -N 100 -L 100 -F 300 -C \
- Butterfly/src/sample_data/RawComps.0/comp0 --stderr -V 18
- dh_auto_test
+ java -cp Butterfly.jar TransAssembly_allProbPaths -N 100 -L 100 -F 300 \
+ -C Butterfly/src/sample_data/RawComps.0/comp0 --stderr -V 18
override_dh_auto_install:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_install \
--
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