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[pkgsrc/trunk]: pkgsrc/biology/hmmer Update to 3.0
details: https://anonhg.NetBSD.org/pkgsrc/rev/7de0085e6078
branches: trunk
changeset: 621986:7de0085e6078
user: wen <wen%pkgsrc.org@localhost>
date: Sun Jul 21 15:58:51 2013 +0000
description:
Update to 3.0
Add LICENSE
Add more distfile mirrors
Upstream changelog please visit:
http://selab.janelia.org/software/hmmer3/3.0/RELEASE-NOTES
diffstat:
biology/hmmer/Makefile | 9 +++-
biology/hmmer/PLIST | 21 +++-------
biology/hmmer/distinfo | 10 ++--
biology/hmmer/patches/patch-aa | 79 +++++++++++------------------------------
4 files changed, 40 insertions(+), 79 deletions(-)
diffs (158 lines):
diff -r 9497cc1a7f87 -r 7de0085e6078 biology/hmmer/Makefile
--- a/biology/hmmer/Makefile Sun Jul 21 15:58:41 2013 +0000
+++ b/biology/hmmer/Makefile Sun Jul 21 15:58:51 2013 +0000
@@ -1,13 +1,16 @@
-# $NetBSD: Makefile,v 1.13 2012/09/11 20:32:12 asau Exp $
+# $NetBSD: Makefile,v 1.14 2013/07/21 15:58:51 wen Exp $
#
-DISTNAME= hmmer-2.3.2
+DISTNAME= hmmer-3.0
CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GENTOO:=distfiles/}
+MASTER_SITES= ${MASTER_SITE_GENTOO:=distfiles/} \
+ http://selab.janelia.org/software/hmmer3/3.0/ \
+ ftp://selab.janelia.org/pub/software/hmmer3/3.0/
MAINTAINER= hdp%cs.nmsu.edu@localhost
HOMEPAGE= http://hmmer.janelia.org/
COMMENT= Implementation of profile HMM software for protein sequence analysis
+LICENSE= gnu-gpl-v3
PKG_INSTALLATION_TYPES= overwrite pkgviews
diff -r 9497cc1a7f87 -r 7de0085e6078 biology/hmmer/PLIST
--- a/biology/hmmer/PLIST Sun Jul 21 15:58:41 2013 +0000
+++ b/biology/hmmer/PLIST Sun Jul 21 15:58:51 2013 +0000
@@ -1,20 +1,13 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $
+@comment $NetBSD: PLIST,v 1.2 2013/07/21 15:58:51 wen Exp $
bin/hmmalign
bin/hmmbuild
-bin/hmmcalibrate
bin/hmmconvert
bin/hmmemit
bin/hmmfetch
-bin/hmmindex
-bin/hmmpfam
+bin/hmmpress
+bin/hmmscan
bin/hmmsearch
-man/man1/hmmalign.1
-man/man1/hmmbuild.1
-man/man1/hmmcalibrate.1
-man/man1/hmmconvert.1
-man/man1/hmmemit.1
-man/man1/hmmer.1
-man/man1/hmmfetch.1
-man/man1/hmmindex.1
-man/man1/hmmpfam.1
-man/man1/hmmsearch.1
+bin/hmmsim
+bin/hmmstat
+bin/jackhmmer
+bin/phmmer
diff -r 9497cc1a7f87 -r 7de0085e6078 biology/hmmer/distinfo
--- a/biology/hmmer/distinfo Sun Jul 21 15:58:41 2013 +0000
+++ b/biology/hmmer/distinfo Sun Jul 21 15:58:51 2013 +0000
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.6 2009/07/16 14:53:19 joerg Exp $
+$NetBSD: distinfo,v 1.7 2013/07/21 15:58:51 wen Exp $
-SHA1 (hmmer-2.3.2.tar.gz) = aa34cb97cbc43ff3bd92dd111ba5677298fe2d40
-RMD160 (hmmer-2.3.2.tar.gz) = 4bf25fc71f332849c76b0a05bca24e88241cee67
-Size (hmmer-2.3.2.tar.gz) = 1024933 bytes
-SHA1 (patch-aa) = 1d5eae739096ec6398e7cd71b92019d76a677d50
+SHA1 (hmmer-3.0.tar.gz) = 77803c0bdb3ab07b7051a4c68c0564de31940c6d
+RMD160 (hmmer-3.0.tar.gz) = 681967fd0d2c0104ca9e080688d9652a187a8b45
+Size (hmmer-3.0.tar.gz) = 3952015 bytes
+SHA1 (patch-aa) = 8d0d3be4401590c20d102b7e0ebadcb1b6c03066
diff -r 9497cc1a7f87 -r 7de0085e6078 biology/hmmer/patches/patch-aa
--- a/biology/hmmer/patches/patch-aa Sun Jul 21 15:58:41 2013 +0000
+++ b/biology/hmmer/patches/patch-aa Sun Jul 21 15:58:51 2013 +0000
@@ -1,63 +1,28 @@
-$NetBSD: patch-aa,v 1.4 2009/07/08 15:20:04 joerg Exp $
-
---- Makefile.in.orig 2003-10-04 21:01:16.000000000 +0200
+$NetBSD: patch-aa,v 1.5 2013/07/21 15:58:51 wen Exp $
+replace "mkdir -p" with ${MKDIR}
+--- Makefile.in.orig 2013-07-21 23:25:33.000000000 +0000
+++ Makefile.in
-@@ -30,11 +30,12 @@ prefix = @prefix@
- exec_prefix = @exec_prefix@
- BINDIR = @bindir@
- MANDIR = @mandir@
-+INSTBIN = ${BSD_INSTALL_PROGRAM}
+@@ -51,7 +51,7 @@ CPPFLAGS = @CPPFLAGS@
- # how to install the man pages;
- # cp is generally fine, unless you preformat your pages.
+ # Other tools
#
-INSTMAN = cp
+INSTMAN = ${BSD_INSTALL_MAN}
- MANSUFFIX = 1
-
- # your compiler and compiler flags
-@@ -109,13 +110,13 @@ src/libhmmer.a:
- # installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
- # Creates these directories if they don't exist.
- install:
-- mkdir -p ${BINDIR}
-- -mkdir -p ${MANDIR}/man${MANSUFFIX}
-+ ${MKDIR} ${DESTDIR}${BINDIR}
-+ -${MKDIR} ${DESTDIR}${MANDIR}/man${MANSUFFIX}
- for file in $(PROGS) $(PVMPROGS); do\
-- cp src/$$file $(BINDIR)/;\
-+ $(INSTBIN) src/$$file ${DESTDIR}$(BINDIR)/;\
- done
- -for file in hmmer $(PROGS); do\
-- $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
-+ $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ AR = @AR@ rcv
+ LN = ln
+ RANLIB = @RANLIB@
+@@ -176,11 +176,11 @@ testsuite: libraries
+ # may be set on a make command line when building contrib RPMs).
+ install: libraries programs
+ cd ${PMARKDIR}; ${MAKE} profmark_progs
+- -mkdir -p ${DESTDIR}${bindir}
++ -${MKDIR} ${DESTDIR}${bindir}
+ for file in $(PROGS); do\
+- cp ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\
++ ${BSD_INSTALL_PROGRAM} ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\
done
-
- # uninstall: Reverses the steps of "make install".
-@@ -133,7 +134,7 @@ uninstall:
- # subdir, remove everything but binaries and Makefiles.
- #
- bindist:
-- mkdir binaries
-+ ${MKDIR} binaries
- for prog in $(PROGS); do\
- (cd binaries; ln -s ../src/$$prog .);\
- done
-@@ -205,7 +206,7 @@ dist:
- # in testsuite.
- #
- cp ssdk/sqc ${BASENAME}-${RELEASE}/testsuite/
-- mkdir ${BASENAME}-${RELEASE}/ssdk
-+ ${MKDIR} ${BASENAME}-${RELEASE}/ssdk
- cp ssdk/rmanprocess.pl ${BASENAME}-${RELEASE}/ssdk/
- #
- # Make the configure scripts from configure.ac
-@@ -288,7 +289,7 @@ dist:
- # directory.
- #
- ftpdist:
-- mkdir -p ${FTPDIR}
-+ ${MKDIR} ${FTPDIR}
- cp -f hmmer-$(RELEASE)/00README ${FTPDIR}
- cp -f hmmer-$(RELEASE)/COPYRIGHT ${FTPDIR}
- cp -f hmmer-$(RELEASE)/INSTALL ${FTPDIR}
+-# -mkdir -p ${DESTDIR}/${MANDIR}/man${MANSUFFIX}
++# -${MKDIR} ${DESTDIR}/${MANDIR}/man${MANSUFFIX}
+ # -for file in hmmer $(PROGS); do\
+ # $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ # done
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