Author: moeller Date: 2011-03-04 16:55:11 +0000 (Fri, 04 Mar 2011) New Revision: 6160
Added: trunk/packages/mira/trunk/debian/docs trunk/packages/mira/trunk/debian/mira-assembler.dirs trunk/packages/mira/trunk/debian/mira-assembler.install trunk/packages/mira/trunk/debian/mira-docs.docs trunk/packages/mira/trunk/debian/mira-examples.examples Removed: trunk/packages/mira/trunk/debian/docs Modified: trunk/packages/mira/trunk/debian/changelog trunk/packages/mira/trunk/debian/control trunk/packages/mira/trunk/debian/rules Log: Mira -- seems to work Modified: trunk/packages/mira/trunk/debian/changelog =================================================================== --- trunk/packages/mira/trunk/debian/changelog 2011-03-03 21:46:38 UTC (rev 6159) +++ trunk/packages/mira/trunk/debian/changelog 2011-03-04 16:55:11 UTC (rev 6160) @@ -1,5 +1,11 @@ -mira (3~rc2-1) UNRELEASED; urgency=low +mira (3.2.1.8-1) UNRELEASED; urgency=low * Initial release (Closes: #435915) + -- Steffen Moeller <[email protected]> Fri, 04 Mar 2011 11:55:25 +0100 + +mira (3~rc2-1) UNRELEASED; urgency=low + + * Initial packaging. + -- Charles Plessy <[email protected]> Tue, 08 Sep 2009 13:35:31 +0900 Modified: trunk/packages/mira/trunk/debian/control =================================================================== --- trunk/packages/mira/trunk/debian/control 2011-03-03 21:46:38 UTC (rev 6159) +++ trunk/packages/mira/trunk/debian/control 2011-03-04 16:55:11 UTC (rev 6160) @@ -4,15 +4,15 @@ 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 -Standards-Version: 3.8.3 +Build-Depends: debhelper (>= 7), autotools-dev, libboost-thread-dev, libexpat1-dev, perl, zlib1g-dev, google-perftools-dev +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 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/ Package: mira-assembler Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, ${misc:Depends}, google-perftools 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 @@ -25,9 +25,42 @@ detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments. + . + 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 + . + 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. + Package: mira-examples Architecture: all Depends: ${misc:Depends} Suggests: mira -Description: +Description: files to experiment with the mira assembler + A series of files to exploit the functionality of mira. + +Package: mira-doc +Architecture: all +Depends: ${misc:Depends} +Suggests: mira +Description: documentation for the mira assembler + An HTML book introducing to mira. Deleted: trunk/packages/mira/trunk/debian/docs =================================================================== --- trunk/packages/mira/trunk/debian/docs 2011-03-03 21:46:38 UTC (rev 6159) +++ trunk/packages/mira/trunk/debian/docs 2011-03-04 16:55:11 UTC (rev 6160) @@ -1,4 +0,0 @@ -NEWS -README -THANKS -HELP_WANTED Added: trunk/packages/mira/trunk/debian/docs =================================================================== --- trunk/packages/mira/trunk/debian/docs (rev 0) +++ trunk/packages/mira/trunk/debian/docs 2011-03-04 16:55:11 UTC (rev 6160) @@ -0,0 +1,5 @@ +NEWS +README +THANKS +HELP_WANTED +ChangeLog Added: trunk/packages/mira/trunk/debian/mira-assembler.dirs =================================================================== --- trunk/packages/mira/trunk/debian/mira-assembler.dirs (rev 0) +++ trunk/packages/mira/trunk/debian/mira-assembler.dirs 2011-03-04 16:55:11 UTC (rev 6160) @@ -0,0 +1 @@ +usr/bin Added: trunk/packages/mira/trunk/debian/mira-assembler.install =================================================================== --- trunk/packages/mira/trunk/debian/mira-assembler.install (rev 0) +++ trunk/packages/mira/trunk/debian/mira-assembler.install 2011-03-04 16:55:11 UTC (rev 6160) @@ -0,0 +1,10 @@ +src/progs/fastatool usr/bin/ +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/ +src/scripts/fastqselect.tcl usr/bin/ Copied: trunk/packages/mira/trunk/debian/mira-docs.docs (from rev 5551, trunk/packages/mira/trunk/debian/docs) =================================================================== --- trunk/packages/mira/trunk/debian/mira-docs.docs (rev 0) +++ trunk/packages/mira/trunk/debian/mira-docs.docs 2011-03-04 16:55:11 UTC (rev 6160) @@ -0,0 +1 @@ +doc Added: trunk/packages/mira/trunk/debian/mira-examples.examples =================================================================== --- trunk/packages/mira/trunk/debian/mira-examples.examples (rev 0) +++ trunk/packages/mira/trunk/debian/mira-examples.examples 2011-03-04 16:55:11 UTC (rev 6160) @@ -0,0 +1 @@ +minidemo Modified: trunk/packages/mira/trunk/debian/rules =================================================================== --- trunk/packages/mira/trunk/debian/rules 2011-03-03 21:46:38 UTC (rev 6159) +++ trunk/packages/mira/trunk/debian/rules 2011-03-04 16:55:11 UTC (rev 6160) @@ -5,3 +5,4 @@ DEB_MAKE_INSTALL_TARGET = install DESTDIR=$(CURDIR)/debian/mira-assembler DEB_MAKE_CHECK_TARGET = check +DEB_CONFIGURE_EXTRA_FLAGS = --enable-minimal _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
