Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv16601
Added Files:
mira.info
Log Message:
copy mira from 10.4 and update to 3.4.1.1
--- NEW FILE: mira.info ---
Package: mira
Version: 3.4.1.1
Revision: 1002
Description: Whole Genome and EST Sequence Assembler
License: GPL
Maintainer: Hanspeter Niederstrasser <nie...@users.sourceforge.net>
Depends: <<
boost1.53.nopython-shlibs,
bzip2-shlibs,
expat1-shlibs (>= 2.0.1-1)
<<
BuildDepends: <<
autoconf2.6,
automake1.13-core,
boost1.53.nopython,
bzip2-dev,
dblatex,
docbook-xsl,
expat1 (>= 2.0.1-1),
fink-package-precedence,
flex-devel,
libxslt-bin
<<
Source: mirror:sourceforge:project/mira-assembler/MIRA/stable/%n-%v.tar.gz
Source-MD5: b76c01dfdf48d929e6c6a509d16ab6b8
Source-Checksum: SHA1(86bcf87f88296df4c3cce1d871e99a5bc3ca1dfd)
PatchScript: <<
mv config/m4 m4
perl -pi -e "s,-pthread,-lpthread,g" configure configure.in
m4/ax_boost_thread.m4 ltmain.sh
<<
GCC: 4.0
SetCPPFLAGS: -I%p/lib/flex/include
SetLDFLAGS: -L%p/lib/flex/lib
ConfigureParams: <<
--mandir=%p/share/man \
--enable-dependency-tracking \
--with-boost=%p \
--with-boost-thread=boost_thread-mt \
--with-boost-regex=boost_regex-mt \
--with-boost-filesystem=boost_filesystem-mt \
--with-boost-iostreams=boost_iostreams-mt \
--with-boost-system=boost_system-mt \
--with-expat=%p \
--disable-static
<<
CompileScript: <<
#!/bin/sh -ev
export PERL=/usr/bin/perl
export PATH=%p/lib/flex/bin:%b/fink:$PATH
export AUTOCONF=%p/bin/autoconf
export ACLOCAL=%p/bin/aclocal-1.13
export AUTOMAKE=%p/bin/automake-1.13
mkdir fink
ln -s %p/lib/flex/bin/flex %b/fink/flex++
autoreconf -vfi
./configure %c
make -w
make -j1 docs
fink-package-precedence .
<<
InstallScript: <<
make install DESTDIR=%d
<<
DocFiles: AUTHORS COPYING ChangeLog GETTING_STARTED HELP_WANTED NEWS README*
THANKS doc/docbook/DefinitiveGuideToMIRA.pdf
Homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/
DescDetail: <<
MIRA - Sequence assembler and mapper for whole genome shotgun and
EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and
IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet.
Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence Assembly
Using Trace Signals and Additional Sequence Information. Computer
Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
<<
DescPort: <<
FlexLexer.h is not in the 10.8 SDK, so make sure we use our flex 2.3.35
(Or use a nasty patch).
Also, our flex doesn't have flex++, so symlink it so avoid version mismatches
http://www.freelists.org/post/mira_talk/Type-mismatch-of-LexerInput-and-LexerOutput-PATCH
<<
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