[med-svn] r15704 - trunk/packages/bitseq/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Wed Jan 1 21:57:36 UTC 2014
Author: tille
Date: 2014-01-01 21:57:36 +0000 (Wed, 01 Jan 2014)
New Revision: 15704
Removed:
trunk/packages/bitseq/trunk/debian/manpages
Modified:
trunk/packages/bitseq/trunk/debian/changelog
trunk/packages/bitseq/trunk/debian/control
trunk/packages/bitseq/trunk/debian/copyright
trunk/packages/bitseq/trunk/debian/rules
trunk/packages/bitseq/trunk/debian/watch
Log:
Create manpages; delete convinience copies of libraries from upstream tarball
Modified: trunk/packages/bitseq/trunk/debian/changelog
===================================================================
--- trunk/packages/bitseq/trunk/debian/changelog 2014-01-01 19:15:07 UTC (rev 15703)
+++ trunk/packages/bitseq/trunk/debian/changelog 2014-01-01 21:57:36 UTC (rev 15704)
@@ -1,4 +1,4 @@
-bitseq (0.7.0-1) UNRELEASED; urgency=medium
+bitseq (0.7.0+dfsg-1) UNRELEASED; urgency=medium
* Initial upload to Debian
Modified: trunk/packages/bitseq/trunk/debian/control
===================================================================
--- trunk/packages/bitseq/trunk/debian/control 2014-01-01 19:15:07 UTC (rev 15703)
+++ trunk/packages/bitseq/trunk/debian/control 2014-01-01 21:57:36 UTC (rev 15704)
@@ -7,7 +7,8 @@
Build-Depends: debhelper (>= 9),
zlib1g-dev,
libbam-dev,
- libboost-dev
+ libboost-dev,
+ help2man
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bitseq/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bitseq/trunk/
Modified: trunk/packages/bitseq/trunk/debian/copyright
===================================================================
--- trunk/packages/bitseq/trunk/debian/copyright 2014-01-01 19:15:07 UTC (rev 15703)
+++ trunk/packages/bitseq/trunk/debian/copyright 2014-01-01 21:57:36 UTC (rev 15704)
@@ -2,6 +2,7 @@
Upstream-Name: BitSeq
Upstream-Contact: Peter Glaus <glaus at cs.man.ac.uk>
Source: https://code.google.com/p/bitseq/downloads/list
+Files-Excluded: boost/ samtools/
Files: *
Copyright: © 2013 Peter Glaus
Deleted: trunk/packages/bitseq/trunk/debian/manpages
===================================================================
--- trunk/packages/bitseq/trunk/debian/manpages 2014-01-01 19:15:07 UTC (rev 15703)
+++ trunk/packages/bitseq/trunk/debian/manpages 2014-01-01 21:57:36 UTC (rev 15704)
@@ -1 +0,0 @@
-debian/mans/*.1
Modified: trunk/packages/bitseq/trunk/debian/rules
===================================================================
--- trunk/packages/bitseq/trunk/debian/rules 2014-01-01 19:15:07 UTC (rev 15703)
+++ trunk/packages/bitseq/trunk/debian/rules 2014-01-01 21:57:36 UTC (rev 15704)
@@ -3,19 +3,61 @@
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
+pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
+mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/
+bindir=$(CURDIR)/debian/$(pkg)/usr/bin/
+
%:
dh $@
-override_dh_builddeb:
- dh_builddeb -- -Z xz
+override_dh_installman:
+ # try to create man pages whereever possible
+ mkdir -p $(mandir)
+ help2man --no-info --name='convert or normalize MCMC expression samples' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/convertSamples > $(mandir)/convertSamples.1
+ help2man --no-info --name='this bitseq module estimates differential expression from data sets' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/estimateDE > $(mandir)/estimateDE.1
+ help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/estimateExpression > $(mandir)/estimateExpression.1
+ help2man --no-info --name='estimate expression dependent hyperparameters for bitseq' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/estimateHyperPar > $(mandir)/estimateHyperPar.1
+ help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/estimateVBExpression > $(mandir)/estimateVBExpression.1
+ help2man --no-info --name='extract MCMC samples of selected transcripts' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/extractSamples > $(mandir)/extractSamples.1
+ help2man --no-info --name='computes log_2 Fold Change from MCMC expression samples' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/getFoldChange > $(mandir)/getFoldChange.1
+ help2man --no-info --name='compute expression of whole genes' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/getGeneExpression > $(mandir)/getGeneExpression.1
+ help2man --no-info --name='compute PPLR from MCMC expression samples' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/getPPLR > $(mandir)/getPPLR.1
+ help2man --no-info --name='estimates variance of MCMC samples' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/getVariance > $(mandir)/getVariance.1
+ help2man --no-info --name='compute relative expression of transcripts within genes' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/getWithinGeneExpression > $(mandir)/getWithinGeneExpression.1
+ help2man --no-info --name='pre\-compute probabilities of (observed) reads'' alignments' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/parseAlignment > $(mandir)/parseAlignment.1
+ help2man --no-info --name='helper for bitseq to transpose files lines and columns' \
+ --version-string="$(version)" --no-discard-stderr \
+ $(bindir)/transposeLargeFile > $(mandir)/transposeLargeFile.1
-override_dh_clean:
- dh_clean
- rm -rf boost samtools
-
-override_dh_auto_clean:
- dh_auto_clean || true
-
override_dh_auto_install:
find -maxdepth 1 -type f -perm /111 -exec dh_install '{}' /usr/bin ';'
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --repack-compression xz --destdir=../tarballs
+
Modified: trunk/packages/bitseq/trunk/debian/watch
===================================================================
--- trunk/packages/bitseq/trunk/debian/watch 2014-01-01 19:15:07 UTC (rev 15703)
+++ trunk/packages/bitseq/trunk/debian/watch 2014-01-01 21:57:36 UTC (rev 15704)
@@ -1,2 +1,4 @@
version=3
-http://code.google.com/p/bitseq/downloads/list .*/files/BitSeq-([0-9.]+).tar.gz
+opts=dversionmangle=s/[~+]dfsg[0-9]*// \
+ http://code.google.com/p/bitseq/downloads/list .*/files/BitSeq-([0-9.]+).tar.gz
+
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