[med-svn] r19066 - trunk/packages/murasaki/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Thu Apr 16 09:15:49 UTC 2015
Author: tille
Date: 2015-04-16 09:15:48 +0000 (Thu, 16 Apr 2015)
New Revision: 19066
Added:
trunk/packages/murasaki/trunk/debian/clean
trunk/packages/murasaki/trunk/debian/murasaki-common.install
trunk/packages/murasaki/trunk/debian/murasaki-mpi.install
trunk/packages/murasaki/trunk/debian/murasaki.install
trunk/packages/murasaki/trunk/debian/murasaki.manpages
Removed:
trunk/packages/murasaki/trunk/debian/install
trunk/packages/murasaki/trunk/debian/manpages
Modified:
trunk/packages/murasaki/trunk/debian/changelog
trunk/packages/murasaki/trunk/debian/control
trunk/packages/murasaki/trunk/debian/rules
Log:
Split up into murasaki and murasaki-mpi (+murasaki-common)
Modified: trunk/packages/murasaki/trunk/debian/changelog
===================================================================
--- trunk/packages/murasaki/trunk/debian/changelog 2015-04-16 06:51:41 UTC (rev 19065)
+++ trunk/packages/murasaki/trunk/debian/changelog 2015-04-16 09:15:48 UTC (rev 19066)
@@ -1,6 +1,7 @@
murasaki (1.68.6-1) UNRELEASED; urgency=medium
* Initial release (Closes: #nnnn)
+ * Split up into murasaki and murasaki-mpi (+murasaki-common)
-- Andreas Tille <tille at debian.org> Thu, 16 Apr 2015 08:51:12 +0200
Added: trunk/packages/murasaki/trunk/debian/clean
===================================================================
--- trunk/packages/murasaki/trunk/debian/clean (rev 0)
+++ trunk/packages/murasaki/trunk/debian/clean 2015-04-16 09:15:48 UTC (rev 19066)
@@ -0,0 +1 @@
+*-mpi
Modified: trunk/packages/murasaki/trunk/debian/control
===================================================================
--- trunk/packages/murasaki/trunk/debian/control 2015-04-16 06:51:41 UTC (rev 19065)
+++ trunk/packages/murasaki/trunk/debian/control 2015-04-16 09:15:48 UTC (rev 19066)
@@ -10,7 +10,8 @@
libterm-readkey-perl,
libtext-wrapper-perl,
libcrypto++-dev,
- libpstreams-dev
+ libpstreams-dev,
+ libopenmpi-dev
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/murasaki/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/murasaki/trunk/
@@ -18,8 +19,51 @@
Package: murasaki
Architecture: any
-Depends: ${shlibs:Depends},
+Depends: murasaki-common,
+ ${shlibs:Depends},
${misc:Depends},
+Description: homology detection tool across multiple large genomes
+ Murasaki is a scalable and fast, language theory-based homology
+ detection tool across multiple large genomes. It enable whole-genome
+ scale multiple genome global alignments. Supports unlimited length
+ gapped-seed patterns and unique TF-IDF based filtering.
+ .
+ Murasaki is an anchor alignment software, which is
+ * exteremely fast (17 CPU hours for whole Human x Mouse genome (with
+ 40 nodes: 52 wall minutes))
+ * scalable (Arbitrarily parallelizable across multiple nodes using MPI.
+ Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
+ * unlimited pattern length
+ * repeat tolerant
+ * intelligent noise reduction
+
+Package: murasaki-mpi
+Architecture: any
+Depends: murasaki-common,
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: homology detection tool across multiple large genomes (MPI-version)
+ Murasaki is a scalable and fast, language theory-based homology
+ detection tool across multiple large genomes. It enable whole-genome
+ scale multiple genome global alignments. Supports unlimited length
+ gapped-seed patterns and unique TF-IDF based filtering.
+ .
+ Murasaki is an anchor alignment software, which is
+ * exteremely fast (17 CPU hours for whole Human x Mouse genome (with
+ 40 nodes: 52 wall minutes))
+ * scalable (Arbitrarily parallelizable across multiple nodes using MPI.
+ Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
+ * unlimited pattern length
+ * repeat tolerant
+ * intelligent noise reduction
+ .
+ This package provides the MPI-enabled binary for murasaki. While this
+ will speed up operation on multi-processor machines it will slow down
+ on a single processor.
+
+Package: murasaki-common
+Architecture: all
+Depends: ${misc:Depends},
${misc:perl},
gnuplot | gnuplot5,
libbio-perl-perl,
@@ -27,7 +71,7 @@
imagemagick
Recommends: libterm-readkey-perl,
libtext-wrapi18n-perl | libtext-wrapper-perl
-Description: homology detection tool across multiple large genomes
+Description: homology detection tool across multiple large genomes (common files)
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
scale multiple genome global alignments. Supports unlimited length
@@ -41,3 +85,6 @@
* unlimited pattern length
* repeat tolerant
* intelligent noise reduction
+ .
+ This package contains all files that are common to the single core murasaki
+ package and the multi core murasaki-mpi package.
Deleted: trunk/packages/murasaki/trunk/debian/install
===================================================================
--- trunk/packages/murasaki/trunk/debian/install 2015-04-16 06:51:41 UTC (rev 19065)
+++ trunk/packages/murasaki/trunk/debian/install 2015-04-16 09:15:48 UTC (rev 19066)
@@ -1,9 +0,0 @@
-*.p[lm] usr/lib/debian-med/bin/
-debian/config.pl usr/share/perl5/murasaki
-perlmodules/* usr/share/perl5/murasaki
-geneparse usr/bin
-mbfa usr/bin
-murasaki usr/bin
-cgr-* usr/lib/murasaki
-testeco usr/lib/murasaki
-align-* usr/lib/murasaki
Deleted: trunk/packages/murasaki/trunk/debian/manpages
===================================================================
--- trunk/packages/murasaki/trunk/debian/manpages 2015-04-16 06:51:41 UTC (rev 19065)
+++ trunk/packages/murasaki/trunk/debian/manpages 2015-04-16 09:15:48 UTC (rev 19066)
@@ -1 +0,0 @@
-doc/*.1
Added: trunk/packages/murasaki/trunk/debian/murasaki-common.install
===================================================================
--- trunk/packages/murasaki/trunk/debian/murasaki-common.install (rev 0)
+++ trunk/packages/murasaki/trunk/debian/murasaki-common.install 2015-04-16 09:15:48 UTC (rev 19066)
@@ -0,0 +1,3 @@
+*.p[lm] usr/lib/debian-med/bin/
+debian/config.pl usr/share/perl5/murasaki
+perlmodules/* usr/share/perl5/murasaki
Added: trunk/packages/murasaki/trunk/debian/murasaki-mpi.install
===================================================================
--- trunk/packages/murasaki/trunk/debian/murasaki-mpi.install (rev 0)
+++ trunk/packages/murasaki/trunk/debian/murasaki-mpi.install 2015-04-16 09:15:48 UTC (rev 19066)
@@ -0,0 +1,6 @@
+geneparse-mpi usr/bin
+mbfa-mpi usr/bin
+murasaki-mpi usr/bin
+cgr-*-mpi usr/lib/murasaki
+testeco-mpi usr/lib/murasaki
+align-*-mpi usr/lib/murasaki
Added: trunk/packages/murasaki/trunk/debian/murasaki.install
===================================================================
--- trunk/packages/murasaki/trunk/debian/murasaki.install (rev 0)
+++ trunk/packages/murasaki/trunk/debian/murasaki.install 2015-04-16 09:15:48 UTC (rev 19066)
@@ -0,0 +1,6 @@
+geneparse usr/bin
+mbfa usr/bin
+murasaki usr/bin
+cgr-* usr/lib/murasaki
+testeco usr/lib/murasaki
+align-* usr/lib/murasaki
Added: trunk/packages/murasaki/trunk/debian/murasaki.manpages
===================================================================
--- trunk/packages/murasaki/trunk/debian/murasaki.manpages (rev 0)
+++ trunk/packages/murasaki/trunk/debian/murasaki.manpages 2015-04-16 09:15:48 UTC (rev 19066)
@@ -0,0 +1 @@
+doc/*.1
Modified: trunk/packages/murasaki/trunk/debian/rules
===================================================================
--- trunk/packages/murasaki/trunk/debian/rules 2015-04-16 06:51:41 UTC (rev 19065)
+++ trunk/packages/murasaki/trunk/debian/rules 2015-04-16 09:15:48 UTC (rev 19066)
@@ -1,18 +1,42 @@
#!/usr/bin/make -f
# debian/rules for murasaki
-# Copyright 2008 Andreas Tille
+# Copyright 2015 Andreas Tille
# GPL
DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-DEBMEDBIN := debian/$(DEBPKGNAME)/usr/lib/debian-med/bin
+DEBMEDBIN := debian/$(DEBPKGNAME)-common/usr/lib/debian-med/bin
MANDIR := debian/$(DEBPKGNAME)/usr/share/man/man1
+CMANDIR := debian/$(DEBPKGNAME)-common/usr/share/man/man1
+MMANDIR := debian/$(DEBPKGNAME)-mpi/usr/share/man/man1
%:
dh $@
+override_dh_auto_build:
+ dh_auto_build -- USE_MPI=YES
+ for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \
+ mv $${bin} $${bin}-mpi ; \
+ done
+ make clean
+ dh_auto_build -- USE_MPI=NO
+
override_dh_installman:
dh_installman
+ # create manpages for PL files
+ mkdir -p $(CMANDIR)
for pscript in $(DEBMEDBIN)/* ; do \
- pod2man $${pscript} > $(MANDIR)/`basename $${pscript}`.1 ; \
+ pod2man $${pscript} > $(CMANDIR)/`basename $${pscript}`.1 ; \
done
- find $(MANDIR) -empty -delete
+ find $(CMANDIR) -empty -delete
+
+override_dh_link:
+ dh_link
+ mkdir -p $(MMANDIR)
+ for man in $(MANDIR)/* ; do \
+ ln -s `basename $${man}`.gz $(MMANDIR)/`basename $${man} .1`-mpi.1.gz ; \
+ done
+
+override_dh_install:
+ dh_install
+ # using wildcards in install files is practical but it duplicates some files
+ find debian/$(DEBPKGNAME)/usr -name "*-mpi" -delete
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