From 2221716cc71064e00cba76b1bfaaf2e37f03eb5b Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Thu, 23 Dec 2004 18:43:28 +0000 Subject: [PATCH] Moved from app-sci/hmmer to sci-biology/hmmer. --- sci-biology/hmmer/ChangeLog | 39 ++++++++++++++++++ sci-biology/hmmer/Manifest | 5 +++ .../hmmer/files/Makefile-hmmer-2.2g.patch | 33 +++++++++++++++ sci-biology/hmmer/files/digest-hmmer-2.3.2 | 1 + sci-biology/hmmer/hmmer-2.3.2.ebuild | 41 +++++++++++++++++++ sci-biology/hmmer/metadata.xml | 6 +++ 6 files changed, 125 insertions(+) create mode 100644 sci-biology/hmmer/ChangeLog create mode 100644 sci-biology/hmmer/Manifest create mode 100644 sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch create mode 100644 sci-biology/hmmer/files/digest-hmmer-2.3.2 create mode 100644 sci-biology/hmmer/hmmer-2.3.2.ebuild create mode 100644 sci-biology/hmmer/metadata.xml diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog new file mode 100644 index 000000000000..c066d0765923 --- /dev/null +++ b/sci-biology/hmmer/ChangeLog @@ -0,0 +1,39 @@ +# ChangeLog for app-sci/hmmer +# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.1 2004/12/23 18:43:28 ribosome Exp $ + +*hmmer-2.3.2 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette +metadata.xml, + +files/Makefile-hmmer-2.2g.patch, +hmmer-2.3.2.ebuild: + Moved from app-sci/hmmer to sci-biology/hmmer. + + 31 Oct 2004; Olivier Fisette -hmmer-2.3.1.ebuild, + hmmer-2.3.2.ebuild: + Added 2.3.2 to x86. Removed old version. + + 17 Oct 2004; David Holm hmmer-2.3.2.ebuild: + Added to ~ppc. + + 14 Oct 2004; Hasan Khalil hmmer-2.3.2.ebuild: + Keyworded ~ppc-macos. + +*hmmer-2.3.2 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette -hmmer-2.2g.ebuild, + +hmmer-2.3.2.ebuild: + New version 2.3.2. Removed old version. + + 18 Nov 2003; Stephen Diener hmmer-2.3.1.ebuild: + ~x86 -> x86 + +*hmmer-2.3.1 (28 Aug 2003) + + 28 Aug 2003; hmmer-2.3.1.ebuild: + Version bump + +*hmmer-2.2g (07 May 2003) + + 07 May 2003; Jon Portnoy hmmer-2.2g.ebuild : + Initial import. Ebuild submitted by Steve Diener and Gontran Zepeda + in bug #20449. diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest new file mode 100644 index 000000000000..cf277751a5e8 --- /dev/null +++ b/sci-biology/hmmer/Manifest @@ -0,0 +1,5 @@ +MD5 ed03b6e6648bd60f1149620f07ae50a9 hmmer-2.3.2.ebuild 914 +MD5 a9bf71231ee1afc22643abab488afea6 ChangeLog 1053 +MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216 +MD5 9fbc129db1a886510ff026fd89e131f1 files/Makefile-hmmer-2.2g.patch 1040 +MD5 355efcc8eaed16353cd1ed41c2d63b4e files/digest-hmmer-2.3.2 64 diff --git a/sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch b/sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch new file mode 100644 index 000000000000..fe9c8fdbcbfa --- /dev/null +++ b/sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch @@ -0,0 +1,33 @@ +--- Makefile.in.orig 2003-05-05 15:21:41.000000000 +0100 ++++ Makefile.in 2003-05-05 15:22:11.000000000 +0100 +@@ -84,6 +84,12 @@ + sindex\ + shuffle\ + sreformat ++SQUIDMANS = afetch\ ++ alistat\ ++ seqstat\ ++ sfetch\ ++ shuffle\ ++ sreformat + + # all: Compile everything (except the testsuite), + # and stick the supported programs in binaries/ +@@ -146,13 +152,14 @@ + for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\ + cp binaries/$$file $(BINDIR)/;\ + done +- for file in hmmer $(PROGS) $(SQUIDPROGS); do\ ++ for file in hmmer $(PROGS); do\ + $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ ++ chmod 0644 $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ + done +- for file in $(SQUIDPROGS); do\ ++ for file in $(SQUIDMANS); do\ + $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ ++ chmod 0644 $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ + done +- + # "make clean" removes almost everything except configuration files + # and binaries. + clean: diff --git a/sci-biology/hmmer/files/digest-hmmer-2.3.2 b/sci-biology/hmmer/files/digest-hmmer-2.3.2 new file mode 100644 index 000000000000..a923f14534a4 --- /dev/null +++ b/sci-biology/hmmer/files/digest-hmmer-2.3.2 @@ -0,0 +1 @@ +MD5 5f073340c0cf761288f961a73821228a hmmer-2.3.2.tar.gz 1024933 diff --git a/sci-biology/hmmer/hmmer-2.3.2.ebuild b/sci-biology/hmmer/hmmer-2.3.2.ebuild new file mode 100644 index 000000000000..d1698c742edb --- /dev/null +++ b/sci-biology/hmmer/hmmer-2.3.2.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2004 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2.ebuild,v 1.1 2004/12/23 18:43:28 ribosome Exp $ + +DESCRIPTION="HMMER - Biological sequence analysis with profile HMMs" +HOMEPAGE="http://hmmer.wustl.edu/" +SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz" +LICENSE="GPL-2" + +SLOT="0" +KEYWORDS="x86 ~ppc-macos ~ppc" +IUSE="" + +src_compile() { + ./configure \ + --host=${CHOST} \ + --prefix=${D}/usr \ + --exec_prefix=${D}/usr \ + --mandir=${D}/usr/share/man || die + +# econf || die + emake || die +} + +src_install() { + einstall || die + + dodoc 00README NOTES + + insinto /usr/share/doc/${PF} + doins Userguide.pdf + + cd squid + + dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate + dolib libsquid.a +} + +src_test() { + make check +} diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml new file mode 100644 index 000000000000..8a4bcd47220d --- /dev/null +++ b/sci-biology/hmmer/metadata.xml @@ -0,0 +1,6 @@ + + + +sci +sediener@gentoo.org + -- 2.26.2