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pkgsrc/biology/hmmer/Makefile

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user-destdir support
2009-07-08 17:14:44 +02:00
# $NetBSD: Makefile,v 1.12 2009/07/08 15:20:04 joerg Exp $
Initial import of hmmer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family.
2003-09-26 05:52:47 +02:00
#
Update hmmer to 2.3.2. Patch provided by David Price in PR pkg/28483. While here, enable pkgviews installation. Changes: -:- hmmsearch intermittently failed on Swissprot searches, on some platforms (reports on AMD/Linux; Mac OS/X). (#h25) -:- hmmpfam memory allocation strategy did not guarantee RAMLIMIT, and could explode to very large allocations when searching with large sequences. (#h26) -:- technical improvements in handing dsq's (digitized sequences); "bug" has no visible effects, except when compiling on different platforms. (#h27) -:- typo fix in P7Forward() recursion; typo may have had minor effect on calculated scores. (#h28) -:- hmmalign now includes --outformat and --oneline option for specifying different output alignment formats than the default Stockholm.
2004-12-01 05:01:09 +01:00
DISTNAME= hmmer-2.3.2
Initial import of hmmer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family.
2003-09-26 05:52:47 +02:00
CATEGORIES= biology
fetch from gentoo mirror.
2009-05-17 01:28:13 +02:00
MASTER_SITES= ${MASTER_SITE_GENTOO:=distfiles/}
Initial import of hmmer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family.
2003-09-26 05:52:47 +02:00
MAINTAINER= hdp@cs.nmsu.edu
update homepage and master site. new master needs active ftp. it doesn't work with EPSV. commented out.
2009-05-17 01:19:19 +02:00
HOMEPAGE= http://hmmer.janelia.org/
Initial import of hmmer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family.
2003-09-26 05:52:47 +02:00
COMMENT= Implementation of profile HMM software for protein sequence analysis
Update hmmer to 2.3.2. Patch provided by David Price in PR pkg/28483. While here, enable pkgviews installation. Changes: -:- hmmsearch intermittently failed on Swissprot searches, on some platforms (reports on AMD/Linux; Mac OS/X). (#h25) -:- hmmpfam memory allocation strategy did not guarantee RAMLIMIT, and could explode to very large allocations when searching with large sequences. (#h26) -:- technical improvements in handing dsq's (digitized sequences); "bug" has no visible effects, except when compiling on different platforms. (#h27) -:- typo fix in P7Forward() recursion; typo may have had minor effect on calculated scores. (#h28) -:- hmmalign now includes --outformat and --oneline option for specifying different output alignment formats than the default Stockholm.
2004-12-01 05:01:09 +01:00
PKG_INSTALLATION_TYPES= overwrite pkgviews
user-destdir support
2009-07-08 17:14:44 +02:00
PKG_DESTDIR_SUPPORT= user-destdir
Update hmmer to 2.3.2. Patch provided by David Price in PR pkg/28483. While here, enable pkgviews installation. Changes: -:- hmmsearch intermittently failed on Swissprot searches, on some platforms (reports on AMD/Linux; Mac OS/X). (#h25) -:- hmmpfam memory allocation strategy did not guarantee RAMLIMIT, and could explode to very large allocations when searching with large sequences. (#h26) -:- technical improvements in handing dsq's (digitized sequences); "bug" has no visible effects, except when compiling on different platforms. (#h27) -:- typo fix in P7Forward() recursion; typo may have had minor effect on calculated scores. (#h28) -:- hmmalign now includes --outformat and --oneline option for specifying different output alignment formats than the default Stockholm.
2004-12-01 05:01:09 +01:00
Initial import of hmmer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family.
2003-09-26 05:52:47 +02:00
GNU_CONFIGURE= yes
Whitespace cleanup, courtesy of pkglint. Patch provided by Sergey Svishchev in private mail.
2007-02-22 20:26:05 +01:00
MAKE_FLAGS+= MKDIR=${MKDIR:Q}
Make hmmer honor $MKDIR for cross-platform install. Addresses pr#26650 from Georg Schwarz.
2004-08-16 04:47:49 +02:00
Initial import of hmmer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes multiple sequence alignement as input and builds statistical model called "Hidden Markov Model" which can be used as a query into a sequence database to find and/or align additional homologues of the sequence family.
2003-09-26 05:52:47 +02:00
.include "../../mk/bsd.pkg.mk"
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