[med-svn] [sambamba] 02/02: Initial Debian packaging
Andreas Tille
tille at debian.org
Sat Mar 4 18:18:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sambamba.
commit ab0f84353627114b2042bea3dd748abd329db42a
Author: Andreas Tille <tille at debian.org>
Date: Sat Mar 4 19:17:59 2017 +0100
Initial Debian packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 24 +++++++++++++++++++++
debian/copyright | 11 ++++++++++
debian/doc-base | 20 ++++++++++++++++++
debian/patches/series | 1 +
debian/patches/use_debian_packaged_libs.patch | 30 +++++++++++++++++++++++++++
debian/rules | 26 +++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++++++
debian/watch | 3 +++
11 files changed, 134 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d8f3fea
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sambamba (0.6.5-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 23 Feb 2017 17:41:31 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b1469dc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: sambamba
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 10),
+ libbiod-dev,
+ liblz4-dev,
+ libhts-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sambamba.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/sambamba.git
+Homepage: https://github.com/lomereiter/sambamba
+
+Package: sambamba
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Tools for working with SAM/BAM data
+ Sambamba provides tools for
+ * Powerful filtering with sambamba view --filter
+ * Picard-like SAM header merging in the merge tool
+ * Optional for operations on whole BAMs
+ * Fast copying of a region to a new file with the slice tool
+ * Duplicate marking/removal, using the Picard criteria
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..3416315
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..5e7e1d4
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,20 @@
+Document: <pkg>
+Title: <title for this doc>
+Author: <author of this doc>
+Abstract: <if you have no better clue the short and
+ long description from debian/control might fit here as well>
+Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+
+# pick one of the below options
+Format: Text
+Files: /usr/share/doc/<pkg>/<pkg>.txt.gz
+
+Format: html
+Index: /usr/share/doc/<pkg>/html/index.html
+Files: /usr/share/doc/<pkg>/html/*
+
+Format: pdf
+Files: /usr/share/doc/<pkg>/<pkg>.pdf.gz
+
+Format: postscript
+Files: /usr/share/doc/<pkg>/<pkg>.ps.gz
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..866f5f9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_libs.patch
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
new file mode 100644
index 0000000..4a2b095
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -0,0 +1,30 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 23 Feb 2017 17:41:31 +0100
+Desciption: Use Debian packaged lz4 and htslib
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,8 +1,7 @@
+ D_COMPILER=dmd
+ D_FLAGS=--compiler=dmd -IBioD -g -d#-O -release -inline # -version=serial
+
+-STATIC_LIB_PATH=-Lhtslib -Llz4/lib
+-STATIC_LIB_SUBCMD=$(STATIC_LIB_PATH) -Wl,-Bstatic -lhts -llz4 -Wl,-Bdynamic
++STATIC_LIB_SUBCMD=-lhts -llz4 -Wl,-Bdynamic
+ RDMD_FLAGS=--force --build-only --compiler=$(D_COMPILER) $(D_FLAGS)
+
+ PLATFORM := $(shell uname -s)
+@@ -12,11 +11,11 @@ LINK_CMD=gcc -dead_strip -lphobos2-ldc -
+ DMD_STATIC_LIBS=htslib/libhts.a lz4/lib/liblz4.a
+ else
+ LINK_CMD=gcc -Wl,--gc-sections -o build/sambamba build/sambamba.o $(STATIC_LIB_SUBCMD) -l:libphobos2-ldc.a -l:libdruntime-ldc.a -lrt -lpthread -lm
+-DMD_STATIC_LIBS=-L-Lhtslib -L-l:libhts.a -L-l:libphobos2.a -L-Llz4/lib -L-l:liblz4.a
++DMD_STATIC_LIBS=-L-l:lhts -L-l:libphobos2.a -L-l:llz4
+ endif
+
+ # DMD only - this goal is used because of fast compilation speed, during development
+-all: htslib-static lz4-static
++all:
+ mkdir -p build/
+ rdmd --force --build-only $(D_FLAGS) $(DMD_STATIC_LIBS) -ofbuild/sambamba main.d
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1ef14d9
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# 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/dpkg/default.mk
+# and use what is set there.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..2a50208
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Artem Tarasov and Albert J. Vilella and Edwin Cuppen and Isaac J. Nijman and Pjotr Prins
+ Title: "Sambamba: fast processing of NGS alignment formats"
+ Journal: Bioinformatics
+ Year: 2015
+ Volume: 31
+ Number: 12
+ Pages: 2032-2034
+ DOI: 10.1093/bioinformatics/btv098
+ PMID: 25697820
+ URL: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv098
+ eprint: https://academic.oup.com/bioinformatics/article-pdf/31/12/2032/568750/btv098.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..dd9fc3c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/lomereiter/sambamba/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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