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mira 4.9.6-2
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Source: mira
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
           Steffen Moeller <moeller@debian.org>,
           Tim Booth <tbooth@ceh.ac.uk>,
           Andreas Tille <tille@debian.org>,
           Thorsten Alteholz <debian@alteholz.de>,
           Michael R. Crusoe <michael.crusoe@gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
               dh-autoreconf,
               autoconf-archive,
               libbz2-dev,
               libexpat1-dev,
               libgoogle-perftools-dev [i386 amd64],
               perl,
               flex,
               libfl-dev,
               vim-common,
               zlib1g-dev,
               libboost-thread-dev,
               libboost-regex-dev,
               libboost-filesystem-dev,
               libboost-system-dev,
               libboost-iostreams-dev
Build-Depends-Indep: docbook-xsl,
                     dblatex
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mira.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/mira.git
Homepage: http://chevreux.org/projects_mira.html

Package: mira-assembler
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends}
Recommends: mira-rfam-12s-rrna
Suggests: mira-doc,
#         mira-examples,
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
 repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
 specialised on reconstructing pristine mRNA transcripts while
 detecting and classifying single nucleotide polymorphisms (SNP)
 occurring in different variations thereof.
 .
 The assembler is routinely used for such various tasks as mutation
 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.
  * mirabait: a "grep" like tool to select reads with kmers up to 256 bases.
  * miraconvert: is a tool to convert, extract and sometimes recalculate all
    kinds of data related to sequence assembly files.

#Package: mira-examples
#Architecture: all
#Depends: ${misc:Depends}
#Suggests: mira-assembler,
#          mira-doc
#Description: files to experiment with the mira assembler
# The mira genome fragment assembler is a specialised assembler for
# sequencing projects classified as 'hard' due to high number of similar
# repeats.
# .
# This package contains a series of files to exploit the functionality
# of mira.

Package: mira-rfam-12s-rrna
Architecture: all
Depends: ${misc:Depends}
Pre-Depends: mira-assembler
Suggests: mira-doc
Description: extract of RFAM 12 rRNA database
 The mira genome fragment assembler is a specialised assembler for
 sequencing projects classified as 'hard' due to high number of similar
 repeats.
 .
 This package contains data to enable MIRA and MIRABAIT to search for rRNA and
 rDNA. This data set contains an excerpt of the RFAM database.

Package: mira-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Suggests: mira-assembler
Description: documentation for the mira assembler
 The mira genome fragment assembler is a specialised assembler for
 sequencing projects classified as 'hard' due to high number of similar
 repeats.
 .
 This package contains an HTML book introducing to mira.