diff options
| -rw-r--r-- | biology/hmmer/Makefile | 9 | ||||
| -rw-r--r-- | biology/hmmer/PLIST | 21 | ||||
| -rw-r--r-- | biology/hmmer/distinfo | 10 | ||||
| -rw-r--r-- | biology/hmmer/patches/patch-aa | 79 |
4 files changed, 40 insertions, 79 deletions
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile index 59668966d32..a3ca8fb3895 100644 --- a/biology/hmmer/Makefile +++ b/biology/hmmer/Makefile @@ -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 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 --git a/biology/hmmer/PLIST b/biology/hmmer/PLIST index 5dd1779c36a..c8b783ad875 100644 --- a/biology/hmmer/PLIST +++ b/biology/hmmer/PLIST @@ -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 --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo index 63b996f454a..80e7f7aaa80 100644 --- a/biology/hmmer/distinfo +++ b/biology/hmmer/distinfo @@ -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 --git a/biology/hmmer/patches/patch-aa b/biology/hmmer/patches/patch-aa index cd1632b55fe..59583dda0f8 100644 --- a/biology/hmmer/patches/patch-aa +++ b/biology/hmmer/patches/patch-aa @@ -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);\ - 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/$$prog .);\ + AR = @AR@ rcv + LN = ln + RANLIB = @RANLIB@ +@@ -176,11 +176,11 @@ testsuite: libraries + # may be set on a make command line when building contrib RPMs). + install: libraries programs + cd ${PMARKDIR}; ${MAKE} profmark_progs +- -mkdir -p ${DESTDIR}${bindir} ++ -${MKDIR} ${DESTDIR}${bindir} + for file in $(PROGS); do\ +- cp ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\ ++ ${BSD_INSTALL_PROGRAM} ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\ done -@@ -205,7 +206,7 @@ dist: - # in testsuite. - # - cp ssdk/sqc ${BASENAME}-${RELEASE}/testsuite/ -- mkdir ${BASENAME}-${RELEASE}/ssdk -+ ${MKDIR} ${BASENAME}-${RELEASE}/ssdk - cp ssdk/rmanprocess.pl ${BASENAME}-${RELEASE}/ssdk/ - # - # Make the configure scripts from configure.ac -@@ -288,7 +289,7 @@ dist: - # directory. - # - ftpdist: -- mkdir -p ${FTPDIR} -+ ${MKDIR} ${FTPDIR} - cp -f hmmer-$(RELEASE)/00README ${FTPDIR} - cp -f hmmer-$(RELEASE)/COPYRIGHT ${FTPDIR} - cp -f hmmer-$(RELEASE)/INSTALL ${FTPDIR} +-# -mkdir -p ${DESTDIR}/${MANDIR}/man${MANSUFFIX} ++# -${MKDIR} ${DESTDIR}/${MANDIR}/man${MANSUFFIX} + # -for file in hmmer $(PROGS); do\ + # $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ + # done |