[med-svn] [manta] 01/01: More Debian like directory layout, demo data in separate package

[Andreas Tille]

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tille pushed a commit to branch master
in repository manta.

commit 6089b745d62131da60c2f0b605a7f1504d9597ea
Author: Andreas Tille <tille at debian.org>
Date:   Sun Feb 12 00:35:23 2017 +0100

    More Debian like directory layout, demo data in separate package
---
 debian/control            | 29 ++++++++++++++++++++++++++++-
 debian/manta-demo.install |  1 +
 debian/manta.install      |  2 ++
 debian/rules              | 20 ++++++++------------
 4 files changed, 39 insertions(+), 13 deletions(-)

diff --git a/debian/control b/debian/control
index 493a512..1f8146d 100644
--- a/debian/control
+++ b/debian/control
@@ -15,6 +15,7 @@ Build-Depends: debhelper (>= 9),
                libboost-chrono-dev,
                libboost-test-dev,
                zlib1g-dev,
+               python-all-dev,
                python-pyflow,
                libhts-dev,
                samtools
@@ -26,7 +27,8 @@ Homepage: https://github.com/Illumina/manta
 Package: manta
 Architecture: any
 Depends: ${shlibs:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         ${python:Depends}
 Description: structural variant and indel caller for mapped sequencing data
  Manta calls structural variants (SVs) and indels from mapped paired-end
  sequencing reads. It is optimized for analysis of germline variation in
@@ -45,3 +47,28 @@ Description: structural variant and indel caller for mapped sequencing data
  analysis of unmatched tumor samples as well. Manta accepts input read
  mappings from BAM or CRAM files and reports all SV and indel inferences
  in VCF 4.1 format.
+
+Package: manta-demo
+Architecture: all
+Depends: ${misc:Depends},
+Suggests: manta
+Description: demo data for manta structural variant and indel caller
+ Manta calls structural variants (SVs) and indels from mapped paired-end
+ sequencing reads. It is optimized for analysis of germline variation in
+ small sets of individuals and somatic variation in tumor/normal sample
+ pairs. Manta discovers, assembles and scores large-scale SVs, medium-
+ sized indels and large insertions within a single efficient workflow.
+ The method is designed for rapid analysis on standard compute hardware:
+ NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a
+ 20 core server, and most WGS tumor/normal analyses can be completed
+ within 2 hours. Manta combines paired and split-read evidence during SV
+ discovery and scoring to improve accuracy, but does not require split-
+ reads or successful breakpoint assemblies to report a variant in cases
+ where there is strong evidence otherwise. It provides scoring models for
+ germline variants in small sets of diploid samples and somatic variants
+ in matched tumor/normal sample pairs. There is experimental support for
+ analysis of unmatched tumor samples as well. Manta accepts input read
+ mappings from BAM or CRAM files and reports all SV and indel inferences
+ in VCF 4.1 format.
+ .
+ This package contains some data for testing manta.
diff --git a/debian/manta-demo.install b/debian/manta-demo.install
new file mode 100644
index 0000000..7fbffb9
--- /dev/null
+++ b/debian/manta-demo.install
@@ -0,0 +1 @@
+usr/share/demo/manta/data	usr/share/doc/manta
diff --git a/debian/manta.install b/debian/manta.install
new file mode 100644
index 0000000..dff9430
--- /dev/null
+++ b/debian/manta.install
@@ -0,0 +1,2 @@
+usr/libexec/*		usr/lib/manta
+usr/lib/python/*	usr/share/manta
diff --git a/debian/rules b/debian/rules
index a65f333..79b3d9e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,18 +3,8 @@
 # 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.
+demopkg        := $(DEBPKGNAME)-demo
 
 # for hardening you might like to uncomment this:
 # export DEB_BUILD_MAINT_OPTIONS=hardening=+all
@@ -22,7 +12,13 @@ DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 CMAKE_EXTRA_FLAGS += -DCMAKE_BUILD_TYPE=Release
 
 %:
-	dh $@ --buildsystem=cmake
+	dh $@ --buildsystem=cmake --with python2
 
 override_dh_auto_configure:
 	DESTDIR=$(CURDIR)/debian/$(DEBPKGNAME) dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
+
+override_dh_auto_install:
+	dh_auto_install
+	find debian -name "*.pyc" -delete
+	# FIXME: better solution: do not Build-Depend: samtools and rather prevent copy of samtools by quilt patch
+	find debian -name "samtools" -delete

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