diff options
author | Steve Price <steve@FreeBSD.org> | 2000-07-10 03:17:40 +0000 |
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committer | Steve Price <steve@FreeBSD.org> | 2000-07-10 03:17:40 +0000 |
commit | 8546beeba575e2efc36f5126f12b5b77167a5bdd (patch) | |
tree | 08306bb513e002977d83d914d14c8e7607ddc76b /biology/clustalw | |
parent | Adding chemeq version 1.10. (diff) |
Adding clustalw version 1.81.
A CLUSTAL W Multiple Sequence Alignment Program.
PR: 19746
Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
Notes
Notes:
svn path=/head/; revision=30406
Diffstat (limited to 'biology/clustalw')
-rw-r--r-- | biology/clustalw/Makefile | 26 | ||||
-rw-r--r-- | biology/clustalw/distinfo | 1 | ||||
-rw-r--r-- | biology/clustalw/files/patch-aa | 11 | ||||
-rw-r--r-- | biology/clustalw/pkg-comment | 1 | ||||
-rw-r--r-- | biology/clustalw/pkg-descr | 24 | ||||
-rw-r--r-- | biology/clustalw/pkg-plist | 3 |
6 files changed, 66 insertions, 0 deletions
diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile new file mode 100644 index 000000000000..5cedd67f3f54 --- /dev/null +++ b/biology/clustalw/Makefile @@ -0,0 +1,26 @@ +# New ports collection makefile for: clustalw +# Date created: 6 July 2000 +# Whom: dbader@eece.unm.edu +# +# $FreeBSD$ +# + +PORTNAME= clustalw +PORTVERSION= 1.81 +CATEGORIES= biology +MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ +DISTNAME= clustalw1.81.UNIX + +MAINTAINER= dbader@eece.unm.edu + +WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} + +do-build: + cd ${WRKSRC} ; ${MAKE} -f makefile + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin + ${MKDIR} ${PREFIX}/share/${PORTNAME} + ${INSTALL_DATA} ${WRKSRC}/clustalw_help ${PREFIX}/share/${PORTNAME} + +.include <bsd.port.mk> diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo new file mode 100644 index 000000000000..030d31087b87 --- /dev/null +++ b/biology/clustalw/distinfo @@ -0,0 +1 @@ +MD5 (clustalw1.81.UNIX.tar.gz) = f239ed842186606ef62529720655ab99 diff --git a/biology/clustalw/files/patch-aa b/biology/clustalw/files/patch-aa new file mode 100644 index 000000000000..d404277773d9 --- /dev/null +++ b/biology/clustalw/files/patch-aa @@ -0,0 +1,11 @@ +--- clustalw.c-orig Wed Jun 7 01:50:05 2000 ++++ clustalw.c Thu Jul 6 20:19:31 2000 +@@ -33,7 +33,7 @@ + #ifdef MSDOS + char *help_file_name = "clustalw.hlp"; + #else +- char *help_file_name = "clustalw_help"; ++ char *help_file_name = "/usr/local/share/clustalw/clustalw_help"; + #endif + + sint max_names; /* maximum length of names in current alignment file */ diff --git a/biology/clustalw/pkg-comment b/biology/clustalw/pkg-comment new file mode 100644 index 000000000000..96dce0a32542 --- /dev/null +++ b/biology/clustalw/pkg-comment @@ -0,0 +1 @@ +CLUSTAL W Multiple Sequence Alignment Program diff --git a/biology/clustalw/pkg-descr b/biology/clustalw/pkg-descr new file mode 100644 index 000000000000..fcb3931270b0 --- /dev/null +++ b/biology/clustalw/pkg-descr @@ -0,0 +1,24 @@ + CLUSTAL W Multiple Sequence Alignment Program + +ClustalW was written by Des Higgins (now at University College, Cork, +Ireland) (des@chah.ucc.ie), Julie Thompson (julie@IGBMC.u-strasbg.fr), +Toby Gibson, (Gibson@EMBL-Heidelberg.DE), and Franc'ois Jeanmougin +(pingouin@igbmc.u-strasbg.fr). It is a complete rewrite and upgrade of +the Clustal and ClustalV packages. which were developed by Des +Higgins. New features include the ability to detect read different +input formats (NBRF/PIR, Fasta, EMBL/Swissprot); align old alignments; +produce phylogenetic trees after alignment (Neighbor Joining trees +with a bootstrap option); write different alignment formats (Clustal, +NBRF/PIR, GCG, PHYLIP); full command line interface. It is described +in the following papers: + + Thompson, J.D., D. G. Higgins and T. J. Gibson. 1994. CLUSTAL W: +improving the sensitivity of progressive multiple sequence alignment +through sequence weighting, positions-specific gap penalties and +weight matrix choice. Nucleic Acids Research 22: 4673-4680. + + Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using +CLUSTAL for multiple sequence alignments. Methods in Enzymology 266: +383-402. + + See URL: www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html diff --git a/biology/clustalw/pkg-plist b/biology/clustalw/pkg-plist new file mode 100644 index 000000000000..32ff2fc3ac77 --- /dev/null +++ b/biology/clustalw/pkg-plist @@ -0,0 +1,3 @@ +bin/clustalw +share/clustalw/clustalw_help +@dirrm share/clustalw |