[med-svn] [bitseq] 07/14: Create manpages; delete convinience copies of libraries from upstream tarball

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository bitseq.

commit 9b5cff5c50f7840cde26caec369351db53a3e190
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jan 1 21:57:36 2014 +0000

    Create manpages; delete convinience copies of libraries from upstream tarball
---
 debian/changelog |  2 +-
 debian/control   |  3 ++-
 debian/copyright |  1 +
 debian/manpages  |  1 -
 debian/rules     | 60 +++++++++++++++++++++++++++++++++++++++++++++++---------
 debian/watch     |  4 +++-
 6 files changed, 58 insertions(+), 13 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 771d686..f004316 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -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
 
diff --git a/debian/control b/debian/control
index 873e130..9603018 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,8 @@ Priority: optional
 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/
diff --git a/debian/copyright b/debian/copyright
index 463ec5b..5e2276e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,6 +2,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 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
diff --git a/debian/manpages b/debian/manpages
deleted file mode 100644
index 4f4649b..0000000
--- a/debian/manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/mans/*.1
diff --git a/debian/rules b/debian/rules
index bb965fd..09fc5bb 100755
--- a/debian/rules
+++ b/debian/rules
@@ -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_clean:
-	dh_clean
-	rm -rf boost samtools
-
-override_dh_auto_clean:
-	dh_auto_clean || true
+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_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
+
diff --git a/debian/watch b/debian/watch
index 15155db..fdecafa 100644
--- a/debian/watch
+++ b/debian/watch
@@ -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
+

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bitseq.git