diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/lagan/Makefile | 54 | ||||
| -rw-r--r-- | biology/lagan/distinfo | 3 | ||||
| -rw-r--r-- | biology/lagan/files/pkg-message.in | 9 | ||||
| -rw-r--r-- | biology/lagan/pkg-descr | 24 | ||||
| -rw-r--r-- | biology/lagan/pkg-plist | 45 |
6 files changed, 136 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index a74ce6572041..c3fd2df0ca3e 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -34,6 +34,7 @@ SUBDIR += hmmer SUBDIR += jalview SUBDIR += kinemage + SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgenome SUBDIR += lsysexp diff --git a/biology/lagan/Makefile b/biology/lagan/Makefile new file mode 100644 index 000000000000..fdec41b76a0d --- /dev/null +++ b/biology/lagan/Makefile @@ -0,0 +1,54 @@ +# New ports collection makefile for: lagan +# Date created: 07 Dec 2005 +# Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> +# +# $FreeBSD$ +# + +PORTNAME= lagan +PORTVERSION= 1.2 +CATEGORIES= biology +MASTER_SITES= http://lagan.stanford.edu/lagan_web/ +DISTNAME= ${PORTNAME}${PORTVERSION:S/.//} + +MAINTAINER= fernan@iib.unsam.edu.ar +COMMENT= Efficient tools for large-scale multiple alignments of genomic DNA + +LAGAN_DIR= ${PREFIX}/${PORTNAME} +USE_PERL5_RUN= yes +SUB_FILES= pkg-message +SUB_LIST= LAGAN_DIR=${LAGAN_DIR} + +EXECUTABLES= anchors chaos glocal mlagan order +SCRIPTS= anal_gloc.pl lagan.pl rechaos.pl slagan.pl +EXEUTILS= Glue bin2bl bin2mf cextract contigorder cstat dotplot fa2xfa \ + getbounds getcontigpos getlength getoverlap rc scorealign \ + scorecontigs seqmerge +SCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \ + mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl + +MAKE_ENV+= CC="${CC} ${CFLAGS}" CPP="${CXX} ${CXXFLAGS}" + +post-patch: + @${REINPLACE_CMD} -E 's,^(CC|CPP) =,\1 ?=,g' \ + ${WRKSRC}/Makefile + +do-install: + @${MKDIR} ${LAGAN_DIR} + ${CP} -R ${WRKSRC}/Readmes ${LAGAN_DIR} +.for exe in ${EXECUTABLES} + ${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${LAGAN_DIR} +.endfor +.for script in ${SCRIPTS} + ${INSTALL_SCRIPT} ${WRKSRC}/${script} ${LAGAN_DIR} +.endfor + @${MKDIR} ${LAGAN_DIR}/utils +.for exeutil in ${EXEUTILS} + ${INSTALL_PROGRAM} ${WRKSRC}/utils/${exeutil} ${LAGAN_DIR}/utils +.endfor +.for scriptutil in ${SCRIPTUTILS} + ${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${LAGAN_DIR}/utils +.endfor + @${CAT} ${PKGMESSAGE} + +.include <bsd.port.mk> diff --git a/biology/lagan/distinfo b/biology/lagan/distinfo new file mode 100644 index 000000000000..c190de38aa90 --- /dev/null +++ b/biology/lagan/distinfo @@ -0,0 +1,3 @@ +MD5 (lagan12.tar.gz) = e45c9287d04b31924115869588f1fb61 +SHA256 (lagan12.tar.gz) = d27754367b3aa9bf34976f7a619d5024be444b47cba370e3f53d0bba87389d4a +SIZE (lagan12.tar.gz) = 112894 diff --git a/biology/lagan/files/pkg-message.in b/biology/lagan/files/pkg-message.in new file mode 100644 index 000000000000..994a417239c8 --- /dev/null +++ b/biology/lagan/files/pkg-message.in @@ -0,0 +1,9 @@ +=============================================================================== + + All the executables, scripts, Readmes and utilities were installed + under %%LAGAN_DIR%% + + Add this to your PATH and set the environment variable + LAGAN_DIR to point to this directory. + +=============================================================================== diff --git a/biology/lagan/pkg-descr b/biology/lagan/pkg-descr new file mode 100644 index 000000000000..33a4aae090be --- /dev/null +++ b/biology/lagan/pkg-descr @@ -0,0 +1,24 @@ +The LAGAN Toolkit consists of four components: + + CHAOS, a pairwise local aligner optimized for non-coding, and other + poorly conserved regions of the genome. + + LAGAN, a highly parametrizable pairwise global alignment using local + alignments generated by CHAOS as anchors. + + Multi-LAGAN, a progressive pairwise algorithm to produce multiple + sequence alignments. + + Shuffle-LAGAN, a novel glocal algorithm that is able to find + rearrangements in a global alignment. + +Fast and sensitive multiple alignment of long genomic sequences. BMC +Bioinformatics 2003 4:66. + +LAGAN and Multi-LAGAN: efficient tools for large-scale multiple +alignment of genomic DNA. Genome Res 2003 13(4): 721-31. + +Glocal alignment: finding rearrangements during alignment. Proceedings +of the ISMB 2003, Bioinformatics 19: 54i-62i. + +WWW: http://lagan.stanford.edu/lagan_web/ diff --git a/biology/lagan/pkg-plist b/biology/lagan/pkg-plist new file mode 100644 index 000000000000..5ee3d3202348 --- /dev/null +++ b/biology/lagan/pkg-plist @@ -0,0 +1,45 @@ +lagan/Readmes/README.mlagan +lagan/Readmes/README.FIRST +lagan/Readmes/README.lagan +lagan/Readmes/README.chaos +lagan/Readmes/README.tools +lagan/Readmes/README.shuffle +lagan/Readmes/LICENSE +lagan/anchors +lagan/chaos +lagan/glocal +lagan/mlagan +lagan/order +lagan/anal_gloc.pl +lagan/lagan.pl +lagan/rechaos.pl +lagan/slagan.pl +lagan/utils/Glue +lagan/utils/bin2bl +lagan/utils/bin2mf +lagan/utils/cextract +lagan/utils/contigorder +lagan/utils/cstat +lagan/utils/dotplot +lagan/utils/fa2xfa +lagan/utils/getbounds +lagan/utils/getcontigpos +lagan/utils/getlength +lagan/utils/getoverlap +lagan/utils/rc +lagan/utils/scorealign +lagan/utils/scorecontigs +lagan/utils/seqmerge +lagan/utils/cmerge2.pl +lagan/utils/draft.pl +lagan/utils/mextract.pl +lagan/utils/mf2bin.pl +lagan/utils/mpretty.pl +lagan/utils/mproject.pl +lagan/utils/mrun.pl +lagan/utils/mrunfile.pl +lagan/utils/mrunpairs.pl +lagan/utils/mviz.pl +@dirrm lagan/Readmes +@dirrmtry lagan/utils +@dirrmtry lagan |