[med-svn] [transdecoder] 01/01: split out docs & sample data to -doc package
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 17 03:57:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository transdecoder.
commit 444bf93ec1815b88bf53772a4cbb59a31f90b310
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Mon Feb 16 22:16:33 2015 -0500
split out docs & sample data to -doc package
---
debian/control | 32 ++++++++++++++++++++--
debian/patches/fix-whatis | 22 +++++++++++++++
debian/patches/series | 1 +
debian/rules | 31 ++++++++++-----------
.../{transdecoder.docs => transdecoder-doc.docs} | 1 +
debian/transdecoder-doc.install | 1 +
debian/transdecoder.install | 3 ++
debian/transdecoder.manpages | 1 +
8 files changed, 73 insertions(+), 19 deletions(-)
diff --git a/debian/control b/debian/control
index f3cbe96..ffb550b 100644
--- a/debian/control
+++ b/debian/control
@@ -3,14 +3,16 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9), cd-hit, liburi-perl
+Build-Depends: debhelper (>= 9),
+ cd-hit,
+ liburi-perl
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/transdecoder.git
Vcs-Git: git://anonscm.debian.org/debian-med/transdecoder.git
Homepage: https://transdecoder.github.io/
Package: transdecoder
-Architecture: any
+Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
cd-hit,
@@ -33,3 +35,29 @@ Description: find coding regions within transcripts
transcript can report multiple ORFs (allowing for operons, chimeras, etc).
* optional the putative peptide has a match to a Pfam domain above the noise
cutoff score.
+
+Package: transdecoder-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+ ${perl:Depends}
+Description: find coding regions within transcripts
+ TransDecoder identifies candidate coding regions within transcript sequences,
+ such as those generated by de novo RNA-Seq transcript assembly using Trinity,
+ or constructed based on RNA-Seq alignments to the genome using Tophat and
+ Cufflinks.
+ .
+ TransDecoder identifies likely coding sequences based on the following
+ criteria:
+ * a minimum length open reading frame (ORF) is found in a transcript sequence
+ * a log-likelihood score similar to what is computed by the GeneID software
+ is > 0.
+ * the above coding score is greatest when the ORF is scored in the 1st
+ reading frame as compared to scores in the other 5 reading frames.
+ * if a candidate ORF is found fully encapsulated by the coordinates of
+ another candidate ORF, the longer one is reported. However, a single
+ transcript can report multiple ORFs (allowing for operons, chimeras, etc).
+ * optional the putative peptide has a match to a Pfam domain above the noise
+ cutoff score.
+ .
+ This package contains the documentation and sample data.
diff --git a/debian/patches/fix-whatis b/debian/patches/fix-whatis
new file mode 100644
index 0000000..c6e5879
--- /dev/null
+++ b/debian/patches/fix-whatis
@@ -0,0 +1,22 @@
+--- a/TransDecoder.LongOrfs
++++ b/TransDecoder.LongOrfs
+@@ -6,7 +6,7 @@
+
+ =head1 NAME
+
+-L<Transdecoder.LongOrfs|http://transdecoder.github.io> - Transcriptome Protein Prediction
++L<Transdecoder.LongOrfs> - Transcriptome Protein Prediction
+
+ =head1 USAGE
+
+--- a/TransDecoder.Predict
++++ b/TransDecoder.Predict
+@@ -4,7 +4,7 @@
+
+ =head1 NAME
+
+-L<Transdecoder|http://transdecoder.sourceforge.net> - Transcriptome Protein Prediction
++L<Transdecoder> - Transcriptome Protein Prediction
+
+ =head1 USAGE
+
diff --git a/debian/patches/series b/debian/patches/series
index 93b3752..69070c7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
cd-hit-est-rename
+fix-whatis
diff --git a/debian/rules b/debian/rules
index 0fefa97..82e914d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,23 +1,11 @@
#!/usr/bin/make -f
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))
-
-# alternatively to manually set those variables you can
-# include /usr/share/cdbs/1/rules/buildvars.mk
-# and use what is set there. Any hint whether dh might set variables in
-# a similar manner are welcome.
+DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
%:
- dh $@
+ dh $@ --parallel
override_dh_auto_clean:
cd ./sample_data && ./cleanme.pl
@@ -25,9 +13,18 @@ override_dh_auto_clean:
override_dh_auto_build:
override_dh_install:
- dh_install TransDecoder* PerlLib util sample_data \
- /usr/lib/transdecoder/
+ dh_install
find debian/transdecoder -name '*.p?' | xargs sed -i \
's=^#!/usr/local/bin/perl=#!/usr/bin/perl='
+
+override_dh_installman:
+ pod2man --section=1 --center="Transcriptome Protein Prediction" \
+ --release="$$VERSION" TransDecoder.LongOrfs > \
+ debian/TransDecoder.LongOrfs.1
+ pod2man --section=1 --center="Transcriptome Protein Prediction" \
+ --release="$$VERSION" TransDecoder.Predict > \
+ debian/TransDecoder.Predict.1
+ dh_installman
+
get-orig-source:
uscan --verbose --force-download --repack --compression xz
diff --git a/debian/transdecoder.docs b/debian/transdecoder-doc.docs
similarity index 68%
rename from debian/transdecoder.docs
rename to debian/transdecoder-doc.docs
index 0fb2340..600b156 100644
--- a/debian/transdecoder.docs
+++ b/debian/transdecoder-doc.docs
@@ -1,2 +1,3 @@
README
debian/tests/run-tests
+Release.Notes
diff --git a/debian/transdecoder-doc.install b/debian/transdecoder-doc.install
new file mode 100644
index 0000000..fa40e5c
--- /dev/null
+++ b/debian/transdecoder-doc.install
@@ -0,0 +1 @@
+sample_data /usr/lib/transdecoder
diff --git a/debian/transdecoder.install b/debian/transdecoder.install
new file mode 100644
index 0000000..59315f1
--- /dev/null
+++ b/debian/transdecoder.install
@@ -0,0 +1,3 @@
+TransDecoder* /usr/lib/transdecoder
+PerlLib /usr/lib/transdecoder
+util /usr/lib/transdecoder
diff --git a/debian/transdecoder.manpages b/debian/transdecoder.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/transdecoder.manpages
@@ -0,0 +1 @@
+debian/*.1
--
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