[med-svn] r16007 - in trunk/packages/spades/trunk/debian: . bin
Andreas Tille
tille at moszumanska.debian.org
Thu Feb 6 20:52:21 UTC 2014
Author: tille
Date: 2014-02-06 20:52:21 +0000 (Thu, 06 Feb 2014)
New Revision: 16007
Added:
trunk/packages/spades/trunk/debian/bin/
trunk/packages/spades/trunk/debian/bin/spades
trunk/packages/spades/trunk/debian/doc-base.dipspades
trunk/packages/spades/trunk/debian/doc-base.spades
trunk/packages/spades/trunk/debian/links
Modified:
trunk/packages/spades/trunk/debian/control
trunk/packages/spades/trunk/debian/rules
Log:
Files layout is a bit hackish but works for the first tests
Added: trunk/packages/spades/trunk/debian/bin/spades
===================================================================
--- trunk/packages/spades/trunk/debian/bin/spades (rev 0)
+++ trunk/packages/spades/trunk/debian/bin/spades 2014-02-06 20:52:21 UTC (rev 16007)
@@ -0,0 +1,6 @@
+#!/bin/sh
+SPADESDIR=/usr/lib/spades/bin
+exename=`basename $0`
+PATH=$SPADESDIR:$PATH
+$SPADESDIR/${exename}.py $@
+
Property changes on: trunk/packages/spades/trunk/debian/bin/spades
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/packages/spades/trunk/debian/control
===================================================================
--- trunk/packages/spades/trunk/debian/control 2014-02-06 08:11:11 UTC (rev 16006)
+++ trunk/packages/spades/trunk/debian/control 2014-02-06 20:52:21 UTC (rev 16007)
@@ -5,7 +5,8 @@
Priority: optional
Build-Depends: debhelper (>= 9),
cmake,
- zlib1g-dev
+ zlib1g-dev,
+ lynx
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/spades/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/spades/trunk/
@@ -14,7 +15,8 @@
Package: spades
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ python
Description: genome assembler for single-cell and isolates data sets
The SPAdes – St. Petersburg genome assembler is intended for both
standard isolates and single-cell MDA bacteria assemblies. It works
Added: trunk/packages/spades/trunk/debian/doc-base.dipspades
===================================================================
--- trunk/packages/spades/trunk/debian/doc-base.dipspades (rev 0)
+++ trunk/packages/spades/trunk/debian/doc-base.dipspades 2014-02-06 20:52:21 UTC (rev 16007)
@@ -0,0 +1,16 @@
+Document: dipspades
+Title: dipSPAdes Manual
+Author: Dmitry Antipov, Anton Bankevich, Alexey Gurevich, a.o.
+Abstract: dipSPAdes is a genome assembler designed specifically for diploid highly
+ polymorphic genomes based on SPAdes. It takes advantage of divergence between
+ haplomes in repetitive genome regions to resolve them and construct longer
+ contigs. dipSPAdes produces consensus contigs (representing a consensus of both
+ haplomes for the orthologous regions) and performs haplotype assembly. Note
+ that dipSPAdes can only benefit from high polymorphism rate (at least 0.4%).
+ For the data with low polymorphism rate no improvement in terms of N50 vs
+ consentional assemblers is expected.
+Section: Science/Biology
+
+Format: html
+Index: /usr/share/doc/spades/dipspades_manual.html
+Files: /usr/share/doc/spades/dipspades_manual.html
Added: trunk/packages/spades/trunk/debian/doc-base.spades
===================================================================
--- trunk/packages/spades/trunk/debian/doc-base.spades (rev 0)
+++ trunk/packages/spades/trunk/debian/doc-base.spades 2014-02-06 20:52:21 UTC (rev 16007)
@@ -0,0 +1,14 @@
+Document: spades
+Title: SPAdes Manual
+Author: Dmitry Antipov, Anton Bankevich, Alexey Gurevich, a.o.
+Abstract: genome assembler for single-cell and isolates data sets
+ The SPAdes – St. Petersburg genome assembler is intended for both
+ standard isolates and single-cell MDA bacteria assemblies. It works
+ with Illumina or IonTorrent reads and is capable of providing hybrid
+ assemblies using PacBio and Sanger reads. You can also provide
+ additional contigs that will be used as long reads.
+Section: Science/Biology
+
+Format: html
+Index: /usr/share/doc/spades/manual.html
+Files: /usr/share/doc/spades/manual.html
Added: trunk/packages/spades/trunk/debian/links
===================================================================
--- trunk/packages/spades/trunk/debian/links (rev 0)
+++ trunk/packages/spades/trunk/debian/links 2014-02-06 20:52:21 UTC (rev 16007)
@@ -0,0 +1 @@
+usr/bin/spades usr/bin/dipspades
Modified: trunk/packages/spades/trunk/debian/rules
===================================================================
--- trunk/packages/spades/trunk/debian/rules 2014-02-06 08:11:11 UTC (rev 16006)
+++ trunk/packages/spades/trunk/debian/rules 2014-02-06 20:52:21 UTC (rev 16007)
@@ -7,7 +7,7 @@
#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 $$2}')
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
#GIT_TAG := $(subst ~,_,$(VERSION))
@@ -22,12 +22,24 @@
%:
dh $@ --sourcedirectory=src --buildsystem=cmake
-override_dh_auto_clean:
- dh_auto_clean
-# rm -rf $(BUILD_DIR)
+override_dh_install:
+ # move those binaries away from /usr/bin that do not need to be called explicitly
+ mkdir -p debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)
+ mv debian/$(DEBPKGNAME)/usr/bin debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)
+ mkdir -p debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/share
+ mv debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME) debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/share
+ # install wrapper
+ cp -a debian/bin debian/$(DEBPKGNAME)/usr/
+ # delete duplocate of license
+ rm -f debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/GPLv2.txt
+ rm -f debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/LICENSE
-xxx_override_dh_auto_build:
- mkdir -p $(BUILD_DIR)
- cd $(BUILD_DIR)
- cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$(PREFIX) $(CURDIR)/src $*
- make -j 8
+override_dh_installdocs:
+ dh_installdocs
+ # move documentation
+ mv debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/share/$(DEBPKGNAME)/*.html debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME)
+
+override_dh_installchangelogs:
+ lynx -dump changelog.html > changelog
+ dh_installchangelogs changelog
+ rm changelog
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