[med-svn] [trinityrnaseq] 02/02: switch to tbooth's package of jaligner
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 16 05:13:59 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 5ef7baaedbb44e90590a145ef236edf43dd23d56
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Sun Feb 15 14:45:02 2015 -0500
switch to tbooth's package of jaligner
The tests aren't unit tests but are integration tests; renaming to match
Tightened up dependencies & file exclusions
Update more hardcoded paths & turn on javahelper
---
debian/control | 6 ++-
debian/copyright | 24 +++++++----
debian/javabuild | 1 +
debian/jlibs | 1 +
debian/patches/update-paths | 71 ++++++++++++++++++++++++++++++--
debian/rules | 26 +++++-------
debian/test/control | 2 +-
debian/test/{run-unit-test => run-tests} | 0
debian/trinityrnaseq.docs | 1 +
debian/trinityrnaseq.install | 2 +-
debian/trinityrnaseq.manifest | 2 +
11 files changed, 104 insertions(+), 32 deletions(-)
diff --git a/debian/control b/debian/control
index 9292f9f..29495d3 100644
--- a/debian/control
+++ b/debian/control
@@ -21,11 +21,11 @@ Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${perl:Depends},
+ ${java:Depends},
bowtie,
python,
libwww-perl,
default-jre-headless,
- libjung-java,
samtools,
jellyfish,
r-base-core,
@@ -33,8 +33,10 @@ Depends: ${shlibs:Depends},
rsem,
express,
trimmomatic,
- transdecoder
+ transdecoder,
+ parafly
Suggests: collectl
+Recommends: ${java:Recommends}
Description: RNA-Seq De novo Assembly
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
diff --git a/debian/copyright b/debian/copyright
index 610f394..d4cd253 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,17 +4,31 @@ Source: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
util/support_scripts/ExitTester.jar
Butterfly/src/lib/*.jar
+ Butterfly/src/src/jaligner/
Butterfly/*.jar
Butterfly/prev_vers
trinity-plugins/rsem*.tar.gz
trinity-plugins/Trimmomatic*
trinity-plugins/parafly*
trinity-plugins/TransDecoder*
+ trinity-plugins/collectl
+ trinity-plugins/GAL*
Files: *
-Copyright: © 2011 The Broad Institute, Inc; © 2014 trinityrnaseq
+Copyright: © 2011 The Broad Institute, Inc
+ © 2014 trinityrnaseq
Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
- trinity-plugins/GAL_0.2.1 is from http://www.sequenceontology.org/software/GAL_Code/
+License: BSD-3-clause
+
+Files: trinity-plugin/*Fastool*
+Copyright: (c) 2012 Francesco Strozzi
+Comment: https://github.com/fstrozzi/Fastool
+License: Expat
+
+Files: debian/*
+Copyright: (c) 2015 Michigan State University
+License: BSD-3-clause
+
License: BSD-3-clause
All rights reserved.
.
@@ -43,9 +57,6 @@ License: BSD-3-clause
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Files: trinity-plugin/*Fastool*
-Copyright: (c) 2012 Francesco Strozzi
-Comment: https://github.com/fstrozzi/Fastool
License: Expat
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
@@ -67,6 +78,3 @@ License: Expat
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
-Files: debian/*
-Copyright: (c) 2015 Michael R. Crusoe, Michigan State University
-License: BSD-3-clause
diff --git a/debian/javabuild b/debian/javabuild
new file mode 100644
index 0000000..fc0ba8b
--- /dev/null
+++ b/debian/javabuild
@@ -0,0 +1 @@
+Butterfly.jar Butterfly/src/src
diff --git a/debian/jlibs b/debian/jlibs
new file mode 100644
index 0000000..6644d13
--- /dev/null
+++ b/debian/jlibs
@@ -0,0 +1 @@
+Butterfly.jar
diff --git a/debian/patches/update-paths b/debian/patches/update-paths
index 2d06b21..02ca370 100644
--- a/debian/patches/update-paths
+++ b/debian/patches/update-paths
@@ -1,6 +1,6 @@
--- trinityrnaseq.orig/util/support_scripts/trinity_install_tests.sh
+++ trinityrnaseq/util/support_scripts/trinity_install_tests.sh
-@@ -6,7 +6,7 @@
+@@ -6,14 +6,14 @@
echo ' '
echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
@@ -9,7 +9,22 @@
then
echo "JellyFish: has been Installed Properly"
else
-@@ -52,7 +52,7 @@
+ 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
@@ -20,8 +35,18 @@
else
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -38,10 +38,10 @@
- my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
+@@ -30,18 +30,18 @@
+ open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
+
+ #directory defnintions
+-my $ROOTDIR = "$FindBin::RealBin";
++my $ROOTDIR = "/usr/lib/trinityrnaseq";
+ my $UTILDIR = "$ROOTDIR/util";
+ my $MISCDIR = "$UTILDIR/misc";
+ my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
+ my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
+-my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
++my $BUTTERFLY_DIR = "/usr/share/java";
my $JELLYFISH_DIR = "/usr";
my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
-my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
@@ -34,3 +59,41 @@
my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
#&version_check();
+@@ -319,7 +319,7 @@
+ ### Butterfly-related options: ####
+ #
+ # --bfly_opts <string> :additional parameters to pass through to butterfly
+-# (see butterfly options: java -jar Butterfly.jar ).
++# (see butterfly options: java -jar /usr/share/java/Butterfly.jar ).
+ # (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).
+ #
+ # //////////////////////////////////
+--- trinityrnaseq.orig/Chrysalis/analysis/Chrysalis.cc
++++ trinityrnaseq/Chrysalis/analysis/Chrysalis.cc
+@@ -258,7 +258,7 @@
+ commandArg<string> iwormStringCmmd("-iworm","inchworm file", "");
+ commandArg<string> oStringCmmd("-o","output directory");
+ commandArg<bool> pairsStringCmmd("-paired", "paired-end reads are used.", false);
+- commandArg<string> butterflyCmmd("-butterfly","butterfly executable", "../Butterfly/Butterfly.jar");
++ commandArg<string> butterflyCmmd("-butterfly","butterfly executable", "/usr/share/java/Butterfly.jar");
+ 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 c23cf4a..5aee352 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,24 +2,14 @@
DH_VERBOSE := 1
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG := $(subst ~,_,$(VERSION))
-
-JAVALIBDIR := /usr/share/java
-export CLASSPATH=${JAVALIBDIR}/collections15.jar:/usr/share/java/gnu-getopt.jar:${JAVALIBDIR}/jung-algorithms.jar:${JAVALIBDIR}/jung-apijar:${JAVALIBDIR}/jung-graph-impl.jar
-
-SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool*
-
+JDIR=/usr/share/java
+export CLASSPATH=${JDIR}/collections15.jar:${JDIR}/gnu-getopt.jar:${JDIR}/jung-algorithms.jar:${JDIR}/jung-api.jar:${JDIR}/jung-graph-impl.jar:${JDIR}/jaligner.jar
+export JAVA_HOME=/usr/lib/jvm/default-java
+SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust
BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq
%:
- dh $@ --parallel
+ dh $@ --parallel --with javahelper
override_dh_auto_configure:
for target in ${SOURCE_DIRECTORIES}; do dh_autotools-dev_updateconfig \
@@ -28,7 +18,6 @@ override_dh_auto_configure:
--prefix=/usr/lib/trinityrnaseq/$${target}; done
override_dh_auto_build:
- jh_build -J Butterfly.jar Butterfly/src
for target in ${SOURCE_DIRECTORIES}; do dh_auto_build \
-O--sourcedirectory=$${target}; done
@@ -38,6 +27,11 @@ override_dh_auto_clean:
--sourcedirectory=$${target}; done
rm Chrysalis/Makefile_auto
+override_dh_auto_test:
+ java -jar Butterfly/Butterfly.jar -N 100 -L 100 -F 300 -C \
+ Butterfly/src/sample_data/RawComps.0/comp0 --stderr -V 18
+ dh_auto_test
+
override_dh_auto_install:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_install \
-O--sourcedirectory=$${target}; done
diff --git a/debian/test/control b/debian/test/control
index 199fb5e..49ad5b9 100644
--- a/debian/test/control
+++ b/debian/test/control
@@ -1,3 +1,3 @@
-Tests: run-unit-test
+Tests: run-tests
Depends: @, @builddeps@
Restrictions: allow-stderr
diff --git a/debian/test/run-unit-test b/debian/test/run-tests
similarity index 100%
rename from debian/test/run-unit-test
rename to debian/test/run-tests
diff --git a/debian/trinityrnaseq.docs b/debian/trinityrnaseq.docs
index 5085989..7791866 100644
--- a/debian/trinityrnaseq.docs
+++ b/debian/trinityrnaseq.docs
@@ -1,2 +1,3 @@
README
Release.Notes
+debian/test/run-tests
diff --git a/debian/trinityrnaseq.install b/debian/trinityrnaseq.install
index 161c278..d824aa2 100644
--- a/debian/trinityrnaseq.install
+++ b/debian/trinityrnaseq.install
@@ -1,7 +1,7 @@
debian/bin/* /usr/bin
Analysis /usr/lib/trinityrnaseq/
-Butterfly/Butterfly.jar /usr/lib/trinityrnaseq/Butterfly/
trinity-plugins/*Fastool*/fastool /usr/lib/trinityrnaseq/trinity-plugins/fastool/
+trinity-plugins/slclust/bin/slclust /usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/
Chrysalis/TranscriptomeFromVaryK /usr/lib/trinityrnaseq/Chrysalis/
Chrysalis/RunButterfly /usr/lib/trinityrnaseq/Chrysalis/
Chrysalis/ReadsToTranscripts_MPI_chang /usr/lib/trinityrnaseq/Chrysalis/
diff --git a/debian/trinityrnaseq.manifest b/debian/trinityrnaseq.manifest
new file mode 100644
index 0000000..acd11d2
--- /dev/null
+++ b/debian/trinityrnaseq.manifest
@@ -0,0 +1,2 @@
+usr/share/java/Butterfly.jar:
+ Main-Class: TransAssembly_allProbPaths
--
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