Moved from app-sci/hmmer to sci-biology/hmmer.

diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
new file mode 100644 (file)
index 0000000..c066d07
--- /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 <ribosome@gentoo.org> +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 <ribosome@gentoo.org> -hmmer-2.3.1.ebuild,
+  hmmer-2.3.2.ebuild:
+  Added 2.3.2 to x86. Removed old version.
+
+  17 Oct 2004; David Holm <dholm@gentoo.org> hmmer-2.3.2.ebuild:
+  Added to ~ppc.
+
+  14 Oct 2004; Hasan Khalil <gongloo@gentoo.org> hmmer-2.3.2.ebuild:
+  Keyworded ~ppc-macos.
+
+*hmmer-2.3.2 (29 Sep 2004)
+
+  29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -hmmer-2.2g.ebuild,
+  +hmmer-2.3.2.ebuild:
+  New version 2.3.2. Removed old version.
+
+  18 Nov 2003; Stephen Diener <sediener@gentoo.org> hmmer-2.3.1.ebuild:
+  ~x86 -> x86
+
+*hmmer-2.3.1 (28 Aug 2003)
+
+  28 Aug 2003; <sediener@gentoo.org> hmmer-2.3.1.ebuild:
+  Version bump
+
+*hmmer-2.2g (07 May 2003)
+
+  07 May 2003; Jon Portnoy <avenj@gentoo.org> 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 (file)
index 0000000..cf27775
--- /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 (file)
index 0000000..fe9c8fd
--- /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 (file)
index 0000000..a923f14
--- /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 (file)
index 0000000..d1698c7
--- /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 (file)
index 0000000..8a4bcd4
--- /dev/null
+++ b/sci-biology/hmmer/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer><email>sediener@gentoo.org</email></maintainer>
+</pkgmetadata>