Author: tbooth-guest
Date: 2014-06-30 08:53:16 +0000 (Mon, 30 Jun 2014)
New Revision: 17340
Added:
trunk/packages/velvet/trunk/debian/VelvetOptimiser.README
trunk/packages/velvet/trunk/debian/velvet-long.install
Modified:
trunk/packages/velvet/trunk/debian/changelog
trunk/packages/velvet/trunk/debian/control
trunk/packages/velvet/trunk/debian/rules
trunk/packages/velvet/trunk/debian/velvet.install
Log:
Sync package with Bio-Linux version. If the changes are accepted as-is, then
VelvetOptimiser should be added to Debian.
Added: trunk/packages/velvet/trunk/debian/VelvetOptimiser.README
===================================================================
--- trunk/packages/velvet/trunk/debian/VelvetOptimiser.README
(rev 0)
+++ trunk/packages/velvet/trunk/debian/VelvetOptimiser.README 2014-06-30
08:53:16 UTC (rev 17340)
@@ -0,0 +1,15 @@
+The VelvetOptimiser script was previously included here as part of the
+Velvet package. However, since there is a newer version available
+as a standalone download it has been packaged separately. To use it,
+install the "velvetoptimiser" package. The script has been renamed and
+put in the path so instead of running
+/usr/share/velvet/contrib/VelvetOptimiser-*/VelvetOptimiser.pl
+it's now simply:
+
+ $ velvetoptimiser
+
+For help:
+
+ $ velvetoptimiser --help |& less
+
+-- Tim Booth, 2013-08-23
Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog 2014-06-30 08:36:48 UTC
(rev 17339)
+++ trunk/packages/velvet/trunk/debian/changelog 2014-06-30 08:53:16 UTC
(rev 17340)
@@ -1,3 +1,15 @@
+velvet (1.2.10+dfsg-1biolinux5) trusty; urgency=low
+
+ * Rebuild for Ubuntu Trusty
+ * Fold in some chages from Bio-Linux
+ * Add velvet-long package as suggested by upstream
+ * Fix TeX deps so manual still builds
+ * Add .c/.h and .pl files to dh_compress exclusions
+ * Ensure that MetaVelvet and VelvetOptimiser sources are excluded
+ as they don't belong in -examples
+
+ -- Tim Booth <[email protected]> Fri, 27 Jun 2014 13:52:48 +0100
+
velvet (1.2.10+dfsg-1) unstable; urgency=low
* New upstream version (+adapted patch)
Modified: trunk/packages/velvet/trunk/debian/control
===================================================================
--- trunk/packages/velvet/trunk/debian/control 2014-06-30 08:36:48 UTC (rev
17339)
+++ trunk/packages/velvet/trunk/debian/control 2014-06-30 08:53:16 UTC (rev
17340)
@@ -7,7 +7,8 @@
Build-Depends: debhelper (>= 9),
zlib1g-dev,
help2man,
- texlive-latex-base
+ texlive-latex-base,
+ texlive-latex-recommended
Standards-Version: 3.9.4
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/velvet/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/velvet/trunk/
@@ -28,6 +29,24 @@
high quality unique contigs. It then uses paired read information, if
available, to retrieve the repeated areas between contigs.
+Package: velvet-long
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ velvet
+Description: Nucleic acid sequence assembler for very short reads, long version
+ Velvet is a de novo genomic assembler specially designed for short read
+ sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and
+ Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near
+ Cambridge, in the United Kingdom.
+ .
+ Velvet currently takes in short read sequences, removes errors then produces
+ high quality unique contigs. It then uses paired read information, if
+ available, to retrieve the repeated areas between contigs.
+ .
+ This package installs special long-mode versions of Velvet, as recommended
+ in the Velvet tutorials.
+
Package: velvet-example
Architecture: all
Depends: ${misc:Depends}
@@ -44,4 +63,3 @@
.
This package contains the example data distributed in the sources of Velvet,
a de novo genomic assembler.
-
Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules 2014-06-30 08:36:48 UTC (rev
17339)
+++ trunk/packages/velvet/trunk/debian/rules 2014-06-30 08:53:16 UTC (rev
17340)
@@ -9,34 +9,61 @@
pkg=velvet
override_dh_auto_clean :
+ # If tarball was not pre-cleaned this will do it.
dh_auto_clean
rm -rf zlib
+ rm -rf third-party
+ rm -rf debian.upstream
+ rm -f *.pdf
+ find -name '._*' -delete
+ rm -rf data.tar.*
-override_dh_auto_build :
+build_long_versions :
+ touch zlib
+ #Make _long version
+ dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1
CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
+ mv velveth velveth_long ; mv velvetg velvetg_long
+ #Make _63 kmer version
+ dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1
CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
+ mv velveth velveth_63 ; mv velvetg velvetg_63
+ #And also one with both options
+ dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth
velvetg OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
+ mv velveth velveth_63_long ; mv velvetg velvetg_63_long
+
+override_dh_auto_build : build_long_versions
touch zlib # prevents the zlib in the ‘third-party’ folder to be built.
dh_auto_build -- OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)"
LDFLAGS="$(LDFLAGS)"
dh_auto_build -- color OPENMP=1 CPPFLAGS="$(CPPFLAGS)"
CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
+ #Pack the examples
+ tar -cvaf data.tar.xz data
override_dh_install :
- mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
+ mkdir -p debian/$(pkg)/usr/share/man/man1/
help2man --no-info --name="simple hashing program" \
- $(CURDIR)/velveth >
$(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth.1
+ ./velveth > debian/$(pkg)/usr/share/man/man1/velveth.1
help2man --no-info --name="simple hashing program (colorspace version)"
\
- $(CURDIR)/velveth_de >
$(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth_de.1
+ ./velveth_de > debian/$(pkg)/usr/share/man/man1/velveth_de.1
help2man --no-info --version-option=" " \
--name="de Bruijn graph construction, error removal and repeat
resolution" \
- $(CURDIR)/velvetg >
$(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg.1
+ ./velvetg > debian/$(pkg)/usr/share/man/man1/velvetg.1
help2man --no-info --version-option=" " \
--name="de Bruijn graph construction, error removal and repeat
resolution (colorspace version)" \
- $(CURDIR)/velvetg_de >
$(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg_de.1
+ ./velvetg_de > debian/$(pkg)/usr/share/man/man1/velvetg_de.1
dh_install
- rm -rf
$(CURDIR)/debian/$(pkg)/usr/share/velvet/contrib/MetaVelvet-v0.3.1/obj
# remove extra copies of GPL
find $(CURDIR)/debian -type f -name 'LICENSE*' -delete
+ #MetaVelvet should be scrubbed, and VelvetOptimiser is now separate.
Note that these
+ #will not have been installed if this was a binarry-only build.
+ [ ! -e debian/velvet-example/usr ] || \
+ rm -r debian/velvet-example/usr/share/doc/velvet/contrib/MetaVelvet*
+ [ ! -e debian/velvet-example/usr ] || { \
+ rm -r
debian/velvet-example/usr/share/doc/velvet/contrib/VelvetOptimiser* && \
+ cp debian/VelvetOptimiser.README
debian/velvet-example/usr/share/doc/velvet/contrib/ \
+ ; }
-#Prevent compression of user manual
+#Prevent compression of user manual and sample code
override_dh_compress :
- dh_compress -X.pdf
+ dh_compress -X.pdf -X.c -X.pl -X.h
override_dh_pysupport :
#Not needed, Python scripts are just for examples
@@ -46,4 +73,3 @@
get-orig-source:
. debian/get-orig-source
-
Added: trunk/packages/velvet/trunk/debian/velvet-long.install
===================================================================
--- trunk/packages/velvet/trunk/debian/velvet-long.install
(rev 0)
+++ trunk/packages/velvet/trunk/debian/velvet-long.install 2014-06-30
08:53:16 UTC (rev 17340)
@@ -0,0 +1,3 @@
+velvet?_63 usr/bin
+velvet?_long usr/bin
+velvet?_63_long usr/bin
Modified: trunk/packages/velvet/trunk/debian/velvet.install
===================================================================
--- trunk/packages/velvet/trunk/debian/velvet.install 2014-06-30 08:36:48 UTC
(rev 17339)
+++ trunk/packages/velvet/trunk/debian/velvet.install 2014-06-30 08:53:16 UTC
(rev 17340)
@@ -1 +1,2 @@
-velvet* usr/bin
+velvet? usr/bin
+velvet?_de usr/bin
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