[med-svn] [trinityrnaseq] 01/02: split out example data to another package
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Sep 17 01:06:36 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 48091206e726e9f0b05d9d500914292ca78690b8
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Sep 16 14:34:56 2015 -0700
split out example data to another package
---
debian/control | 20 +++++++++-
debian/copyright | 50 +++++++++++++++++++++++++
debian/lintian-overrides | 2 -
debian/rules | 3 +-
debian/trinityrnaseq-examples.install | 1 +
debian/trinityrnaseq-examples.lintian-overrides | 2 +
debian/trinityrnaseq.install | 1 -
debian/{jlibs => trinityrnaseq.jlibs} | 0
debian/trinityrnaseq.lintian-overrides | 1 +
9 files changed, 75 insertions(+), 5 deletions(-)
diff --git a/debian/control b/debian/control
index 637dfd2..e071880 100644
--- a/debian/control
+++ b/debian/control
@@ -41,7 +41,7 @@ Depends: ${shlibs:Depends},
parafly,
curl
Suggests: collectl
-Recommends: ${java:Recommends}
+Recommends: ${java:Recommends}, trinityrnaseq-examples
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
@@ -51,3 +51,21 @@ Description: RNA-Seq De novo Assembly
transcriptional complexity at a given gene or locus, and then processes
each graph independently to extract full-length splicing isoforms and to tease
apart transcripts derived from paralogous genes.
+
+Package: trinityrnaseq-examples
+Architecture: all
+Depends: ${perl:Depends},
+ ${java:Depends},
+ ${misc:Depends}
+Recommends: trinityrnaseq
+Description: RNA-Seq De novo Assembly common example and testing files
+ Trinity represents a novel method for the efficient and robust de novo
+ reconstruction of transcriptomes from RNA-seq data. Trinity combines three
+ independent software modules: Inchworm, Chrysalis, and Butterfly, applied
+ sequentially to process large volumes of RNA-seq reads. Trinity partitions
+ the sequence data into many individual de Bruijn graphs, each representing the
+ transcriptional complexity at a given gene or locus, and then processes
+ each graph independently to extract full-length splicing isoforms and to tease
+ apart transcripts derived from paralogous genes.
+ .
+ This package contains testing & example files.
diff --git a/debian/copyright b/debian/copyright
index bebb07c..0af1d51 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -22,6 +22,14 @@ Copyright: © 2011 The Broad Institute, Inc
Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
License: BSD-3-clause
+Files: Butterfly/src/src/NWalign.java
+Copyright: Ahmed Moustafa <ahmed at users.sf.net>
+License: GPL-2+
+
+Files: trinity-plugins/*Fastool*/kseq.h
+Copyright: (c) 2008 Genome Research Ltd (GRL).
+License: MIT
+
Files: trinity-plugins/*Fastool*
Copyright: (c) 2012 Francesco Strozzi
Comment: https://github.com/fstrozzi/Fastool
@@ -80,3 +88,45 @@ License: Expat
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
+License: GPL-2+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
deleted file mode 100644
index 3cb29c6..0000000
--- a/debian/lintian-overrides
+++ /dev/null
@@ -1,2 +0,0 @@
-trinityrnaseq: executable-not-elf-or-script usr/lib/trinityrnaseq/*
-trinityrnaseq: image-file-in-usr-lib usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/*
diff --git a/debian/rules b/debian/rules
index 5892085..0914720 100755
--- a/debian/rules
+++ b/debian/rules
@@ -26,7 +26,8 @@ override_dh_auto_build:
override_dh_auto_clean:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_clean \
--sourcedirectory=$${target}; done
- rm Chrysalis/Makefile_auto
+ rm --force Chrysalis/Makefile_auto
+ rm --force trinity-plugins/slclust/bin/slclust
override_dh_auto_test:
java -cp Butterfly.jar TransAssembly_allProbPaths -N 100 -L 100 -F 300 \
diff --git a/debian/trinityrnaseq-examples.install b/debian/trinityrnaseq-examples.install
new file mode 100644
index 0000000..6c8c1c4
--- /dev/null
+++ b/debian/trinityrnaseq-examples.install
@@ -0,0 +1 @@
+sample_data /usr/lib/trinityrnaseq/
diff --git a/debian/trinityrnaseq-examples.lintian-overrides b/debian/trinityrnaseq-examples.lintian-overrides
new file mode 100644
index 0000000..2d13570
--- /dev/null
+++ b/debian/trinityrnaseq-examples.lintian-overrides
@@ -0,0 +1,2 @@
+trinityrnaseq-examples: image-file-in-usr-lib usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/*
+trinityrnaseq-examples: executable-not-elf-or-script usr/lib/trinityrnaseq/*
diff --git a/debian/trinityrnaseq.install b/debian/trinityrnaseq.install
index 8c6270f..113aa84 100644
--- a/debian/trinityrnaseq.install
+++ b/debian/trinityrnaseq.install
@@ -17,5 +17,4 @@ Chrysalis/Chrysalis /usr/lib/trinityrnaseq/Chrysalis/
Chrysalis/BreakTransByPairs /usr/lib/trinityrnaseq/Chrysalis/
Trinity /usr/lib/trinityrnaseq
PerlLib /usr/lib/trinityrnaseq/
-sample_data /usr/lib/trinityrnaseq/
util /usr/lib/trinityrnaseq/
diff --git a/debian/jlibs b/debian/trinityrnaseq.jlibs
similarity index 100%
rename from debian/jlibs
rename to debian/trinityrnaseq.jlibs
diff --git a/debian/trinityrnaseq.lintian-overrides b/debian/trinityrnaseq.lintian-overrides
new file mode 100644
index 0000000..19e50fa
--- /dev/null
+++ b/debian/trinityrnaseq.lintian-overrides
@@ -0,0 +1 @@
+trinityrnaseq: executable-not-elf-or-script usr/lib/trinityrnaseq/*
--
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