[med-svn] r6160 - trunk/packages/mira/trunk/debian

Steffen Möller moeller at alioth.debian.org
Fri Mar 4 16:55:14 UTC 2011 

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 <moeller at debian.org>  Fri, 04 Mar 2011 11:55:25 +0100
+
+mira (3~rc2-1) UNRELEASED; urgency=low
+
+  * Initial packaging.
+
  -- Charles Plessy <plessy at debian.org>  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 <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
-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

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