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 <[email protected]> Sun, 5 Aug 2007 14:01:14 +0900 + Steffen Moeller <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> DM-Upload-Allowed: yes Uploaders: Charles Plessy <[email protected]> -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 =================================================================== _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
