Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv1280
Added Files:
breseq.info
Log Message:
new pkg breseq 0.23
--- NEW FILE: breseq.info ---
Package: breseq
Version: 0.23
Revision: 1
Description: Mutation finder in microbe evolution
License: GPL
Maintainer: Hanspeter Niederstrasser <nie...@users.sourceforge.net>
Depends: <<
bowtie2 (>= 2.1.0),
gcc48-shlibs,
libncurses5-shlibs,
r-base
<<
BuildDepends: <<
fink-package-precedence,
gcc48-compiler,
libncurses5-dev
<<
Source: http://breseq.googlecode.com/files/breseq-%v.tar.gz
Source-MD5: 7bc50720d090c1fd30c423f80ea70c0f
Source-Checksum: SHA1(b1ee6a6fbe317b8977da0b714db5f1c9d00f751c)
SetCC: gcc-fsf-4.8
SetCXX: g++-fsf-4.8
#UseMaxBuildJobs: false
ConfigureParams: <<
--enable-dependency-tracking \
--disable-static \
--prefix=%p/lib/breseq
<<
GCC: 4.0
CompileScript: <<
%{default_script}
fink-package-precedence .
<<
InfoTest: <<
TestScript: make test || exit 2
<<
InstallScript: <<
make install DESTDIR=%d
# don't need the header
rm -r %i/lib/breseq/include
# make a symlink in %p/bin
install -m 0755 -d %i/bin
ln -s %p/lib/breseq/bin/breseq %i/bin/breseq
<<
DocFiles: AUTHORS COPYING NEWS README
ConfFiles: <<
%p/lib/breseq/share/breseq/combined_circos.conf
%p/lib/breseq/share/breseq/ideogram.conf
%p/lib/breseq/share/breseq/indels.conf
%p/lib/breseq/share/breseq/karyotype.and.layout.conf
%p/lib/breseq/share/breseq/mobs.conf
<<
Homepage: http://code.google.com/p/breseq/
DescDetail: <<
breseq is a computational pipeline for finding mutations relative to a
reference sequence in short-read DNA re-sequencing data intended for
haploid microbial genomes (<20 Mb). breseq is a command line tool
implemented in C++ and R.
It reports single-nucleotide mutations, point insertions and deletions,
large deletions, and new junctions supported by mosaic reads (such as
those produced by new mobile element insertions) in an annotated HTML
format.
<<
DescPackaging: <<
Build fails with clang
http://code.google.com/p/breseq/issues/detail?id=66
so using gcc48 until that is fixed (not as of 0.24rc1).
Stashed in private directory because it packages its own copy of
samtools which collides with the real samtools.
<<
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