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 <[email protected]> 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 <[email protected]> +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/* -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
