[med-svn] r7506 - in trunk/packages/mira/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Fri Aug 19 17:37:37 UTC 2011
Author: tbooth-guest
Date: 2011-08-19 17:37:37 +0000 (Fri, 19 Aug 2011)
New Revision: 7506
Added:
trunk/packages/mira/trunk/debian/README.source
trunk/packages/mira/trunk/debian/mira-doc.README.Debian
trunk/packages/mira/trunk/debian/mira-doc.docs
trunk/packages/mira/trunk/debian/patches/
trunk/packages/mira/trunk/debian/patches/add_shebang_lines
trunk/packages/mira/trunk/debian/patches/series
trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build
trunk/packages/mira/trunk/debian/stamp-autotools-files
trunk/packages/mira/trunk/debian/stamp-makefile-build
trunk/packages/mira/trunk/debian/stamp-makefile-check
Modified:
trunk/packages/mira/trunk/debian/changelog
trunk/packages/mira/trunk/debian/control
trunk/packages/mira/trunk/debian/mira-assembler.install
trunk/packages/mira/trunk/debian/rules
Log:
Some fairly major work on this package, as it's important to Bio-Linux users.
I've still not got the documentation building part sorted 100% but most
other things look good to me.
Note there is also a package sitting in Git - I made a note on there that this
is the latest version. Will work on this again next week - I suggest waiting
for the final release before pushing to Debian in any case.
Added: trunk/packages/mira/trunk/debian/README.source
===================================================================
--- trunk/packages/mira/trunk/debian/README.source (rev 0)
+++ trunk/packages/mira/trunk/debian/README.source 2011-08-19 17:37:37 UTC (rev 7506)
@@ -0,0 +1,15 @@
+mira for Debian
+---------------
+
+Basic packaging seems fine. There are issues with the location of
+Google's tcmalloc library.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 5 Aug 2007 14:01:14 +0900
+ Steffen Moeller <moeller at debian.org> Fri, 04 Mar 2011 17:39:07 +0100
+
+Further to the above, on Sid right now it looks like this should build fine with a
+build dependency on libgoogle-perftools-dev and a runtime dependency on
+libtcmalloc-minimal0. However, backporting this package to Lucid is a non-starter
+so instead I've made it build against the runtime.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 18 Aug 2011 11:34:11 +0100
Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog 2011-08-19 17:34:26 UTC (rev 7505)
+++ trunk/packages/mira/trunk/debian/changelog 2011-08-19 17:37:37 UTC (rev 7506)
@@ -1,3 +1,12 @@
+mira (3.4rc3-2) lucid; urgency=low
+
+ * Version 3.2.1.8 has been removed from SF.net. Packaging the
+ latest RC instead.
+ * Fixed linking against tcmalloc (see README)
+ * Fixed build of docs - HTML is installed in mira-doc
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 19 Aug 2011 12:35:12 +0100
+
mira (3.2.1.8-1) UNRELEASED; urgency=low
* Initial release (Closes: #435915)
Modified: trunk/packages/mira/trunk/debian/control
===================================================================
--- trunk/packages/mira/trunk/debian/control 2011-08-19 17:34:26 UTC (rev 7505)
+++ trunk/packages/mira/trunk/debian/control 2011-08-19 17:37:37 UTC (rev 7506)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7), autotools-dev, libboost-thread-dev, libexpat1-dev, perl, zlib1g-dev, libtcmalloc-minimal0
+Build-Depends: debhelper (>= 7), autotools-dev, libboost-thread-dev, libexpat1-dev, perl, zlib1g-dev, libtcmalloc-minimal0, dblatex, docbook-xsl
Standards-Version: 3.9.1
Homepage: http://chevreux.org/projects_mira.html
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/?rev=0&sc=0
@@ -13,6 +13,7 @@
Package: mira-assembler
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, libtcmalloc-minimal0
+Suggests: mira-examples, mira-doc
Description: Whole Genome Shotgun and EST Sequence Assembler
The mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
@@ -28,27 +29,27 @@
.
The package provides the following executables:
Binaries provided:
- - mira: for assembly of genome sequences
- - miramem: estimating memory needed to assemble projects. Realised through
- link to mira.
- - convert_project: for converting project file types into other types
- - caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
- frequently used file converters (realised through links to convert_project)
- - scftool: set of tools useful when working with SCF trace files
- - fastatool: set of tools useful when working with FASTA trace files
+ - mira: for assembly of genome sequences
+ - miramem: estimating memory needed to assemble projects. Realised through
+ link to mira.
+ - convert_project: for converting project file types into other types
+ - caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
+ frequently used file converters (realised through links to convert_project)
+ - scftool: set of tools useful when working with SCF trace files
+ - fastatool: set of tools useful when working with FASTA trace files
.
Scripts provided:
- - fasta2frag.tcl: fragmenting sequences into smaller, overlapping
- subsequences. Useful for simulating shotgun sequences. Can create
- subsequences in both directions (/default) and also paired-end sequences.
- - fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
- a file with names of reads, select the sequences from the input FASTA (and
- quality file) and writes them to an output FASTA
- - fastqselect.tcl: like fastaselect.tcl, only for FASTQ
- - fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
- consensus tags in ACE files written by the MIRA assembler (and possibly
- other programs). This script massages an ACE file so that consed can read
- the consensus tags.
+ - fasta2frag.tcl: fragmenting sequences into smaller, overlapping
+ subsequences. Useful for simulating shotgun sequences. Can create
+ subsequences in both directions (/default) and also paired-end sequences.
+ - fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
+ a file with names of reads, select the sequences from the input FASTA (and
+ quality file) and writes them to an output FASTA
+ - fastqselect.tcl: like fastaselect.tcl, only for FASTQ
+ - fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
+ consensus tags in ACE files written by the MIRA assembler (and possibly
+ other programs). This script massages an ACE file so that consed can read
+ the consensus tags.
Package: mira-examples
@@ -59,6 +60,7 @@
A series of files to exploit the functionality of mira.
Package: mira-doc
+Section: doc
Architecture: all
Depends: ${misc:Depends}
Suggests: mira
Modified: trunk/packages/mira/trunk/debian/mira-assembler.install
===================================================================
--- trunk/packages/mira/trunk/debian/mira-assembler.install 2011-08-19 17:34:26 UTC (rev 7505)
+++ trunk/packages/mira/trunk/debian/mira-assembler.install 2011-08-19 17:37:37 UTC (rev 7506)
@@ -2,8 +2,6 @@
src/progs/mira usr/bin/
src/progs/scftool usr/bin/
src/progs/sw usr/bin/
-src/progs/miratest usr/bin/
-src/progs/extractContigsFromCAF usr/bin/
src/progs/convert_project usr/bin/
src/scripts/fasta2frag.tcl usr/bin/
src/scripts/fastaselect.tcl usr/bin/
Added: trunk/packages/mira/trunk/debian/mira-doc.README.Debian
===================================================================
--- trunk/packages/mira/trunk/debian/mira-doc.README.Debian (rev 0)
+++ trunk/packages/mira/trunk/debian/mira-doc.README.Debian 2011-08-19 17:37:37 UTC (rev 7506)
@@ -0,0 +1,4 @@
+This package provides the Definitive Guide To MIRA book, which is included with
+the default MIRA download, in HTML format.
+
+See: /usr/share/doc/mira/DefinitiveGuideToMIRA.html
Added: trunk/packages/mira/trunk/debian/mira-doc.docs
===================================================================
--- trunk/packages/mira/trunk/debian/mira-doc.docs (rev 0)
+++ trunk/packages/mira/trunk/debian/mira-doc.docs 2011-08-19 17:37:37 UTC (rev 7506)
@@ -0,0 +1 @@
+doc/
Added: trunk/packages/mira/trunk/debian/patches/add_shebang_lines
===================================================================
--- trunk/packages/mira/trunk/debian/patches/add_shebang_lines (rev 0)
+++ trunk/packages/mira/trunk/debian/patches/add_shebang_lines 2011-08-19 17:37:37 UTC (rev 7506)
@@ -0,0 +1,27 @@
+#Add a missing #! line to 2 demo scripts just to please Lintian
+--- a/minidemo/solexa1/runme.sh
++++ b/minidemo/solexa1/runme.sh
+@@ -1,7 +1,8 @@
++#!/bin/sh
+
+ ln -s ../data/solexa_eco_art/ecoli_* .
+
+ mira --project=ecoli --job=mapping,genome,normal,solexa --fasta -AS:nop=1 -SB:bsn=ecoli_k12_mg1655 -SB:lsd=yes:bft=gbf SOLEXA_SETTINGS -AL:mrs=60:shme=5 | tee log_assembly.txt
+
+ echo
+-echo "Please read the README to know what is in the results."
+\ No newline at end of file
++echo "Please read the README to know what is in the results."
+--- a/minidemo/solexa2/runme.sh
++++ b/minidemo/solexa2/runme.sh
+@@ -1,7 +1,8 @@
++#!/bin/sh
+
+ ln -s ../data/solexa_eco_art/ecoli_*fasta* .
+
+ mira --project=ecoli --job=denovo,genome,normal,solexa --fasta | tee log_assembly.txt
+
+ echo
+-echo "This was a de-novo assembly of Solexa reads."
+\ No newline at end of file
++echo "This was a de-novo assembly of Solexa reads."
Added: trunk/packages/mira/trunk/debian/patches/series
===================================================================
--- trunk/packages/mira/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mira/trunk/debian/patches/series 2011-08-19 17:37:37 UTC (rev 7506)
@@ -0,0 +1,2 @@
+add_shebang_lines
+xsltproc_nonet_for_doc_build
Added: trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build
===================================================================
--- trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build (rev 0)
+++ trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build 2011-08-19 17:37:37 UTC (rev 7506)
@@ -0,0 +1,21 @@
+# Makes sure the documentation builds without needing network access.
+# This magically works if docbook-xsl is installed, otherwise it fails
+# complaining that it needs to access http://docbook.sourceforge.net/release/xsl/current/html/docbook.xsl
+
+--- a/doc/docbook/Makefile.in
++++ b/doc/docbook/Makefile.in
+@@ -385,12 +385,12 @@
+
+ %_part.html: %_part.xml
+ @echo "Making .html out of _part.xml" $@
+- @$(SHELL) -ec 'xsltproc --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<'
++ $(SHELL) -ec 'xsltproc --nonet --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<'
+
+ chapters: ${CHAP_HTML}
+
+ books: ${CHAP_XML} book_definitiveguide.xml
+- xsltproc --xinclude --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml
++ xsltproc --xinclude --nonet --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml
+ dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf $(top_srcdir)/doc/docbook/book_definitiveguide.xml
+
+ all: chapters books
Modified: trunk/packages/mira/trunk/debian/rules
===================================================================
--- trunk/packages/mira/trunk/debian/rules 2011-08-19 17:34:26 UTC (rev 7505)
+++ trunk/packages/mira/trunk/debian/rules 2011-08-19 17:37:37 UTC (rev 7506)
@@ -1,8 +1,45 @@
#!/usr/bin/make -f
-include /usr/share/cdbs/1/class/autotools.mk
-include /usr/share/cdbs/1/rules/debhelper.mk
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
-DEB_MAKE_INSTALL_TARGET = install DESTDIR=$(CURDIR)/debian/mira-assembler
-DEB_MAKE_CHECK_TARGET = check
-DEB_CONFIGURE_EXTRA_FLAGS = --enable-minimal
+%:
+ dh $@ --with quilt
+
+override_dh_auto_install :
+ make install DESTDIR=$(CURDIR)/debian/mira-assembler
+ #There is no installation target for the docs
+ mkdir -p $(CURDIR)/debian/tmp/doc
+ cp -r -t $(CURDIR)/debian/tmp/doc doc/docbook/bookfigures doc/docbook/images \
+ doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true
+
+override_dh_auto_test:
+ make check
+
+#Make the docs
+override_dh_auto_build:
+ dh_auto_build
+ifneq (,$(findstring mira-doc, $(shell dh_listpackages)))
+ dh_auto_build --sourcedir=doc
+endif
+
+#Remove unneeded .tcl extensions from scripts
+override_dh_install:
+ dh_install
+ if [ -d debian/mira-assembler ] ; then \
+ for f in $$(ls debian/mira-assembler/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \
+ fi
+
+#Hacky thing to allow building against tcmalloc without installing
+#troublesome libbgoogle-perftools-dev, see README.Debian
+export LDFLAGS=-L$(CURDIR)/lib
+
+override_dh_clean:
+ dh_clean
+ rm -rf lib
+
+override_dh_auto_configure :
+ mkdir lib
+ ln -s /usr/lib/libtcmalloc_minimal.so.0 lib/libtcmalloc_minimal.so
+ dh_auto_configure
+
Added: trunk/packages/mira/trunk/debian/stamp-autotools-files
===================================================================
Added: trunk/packages/mira/trunk/debian/stamp-makefile-build
===================================================================
Added: trunk/packages/mira/trunk/debian/stamp-makefile-check
===================================================================
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