Moving to sci-biology/hmmer

6 files changed, 0 insertions, 119 deletions

diff --git a/app-sci/hmmer/ChangeLog b/app-sci/hmmer/ChangeLog
deleted file mode 100644
index 6f0396940559..000000000000
--- a/app-sci/hmmer/ChangeLog
+++ /dev/null
@@ -1,33 +0,0 @@
-# ChangeLog for app-sci/hmmer
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/hmmer/ChangeLog,v 1.8 2004/11/01 01:53:06 ribosome Exp $
-
-  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/app-sci/hmmer/Manifest b/app-sci/hmmer/Manifest
deleted file mode 100644
index cf277751a5e8..000000000000
--- a/app-sci/hmmer/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-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/app-sci/hmmer/files/Makefile-hmmer-2.2g.patch b/app-sci/hmmer/files/Makefile-hmmer-2.2g.patch
deleted file mode 100644
index fe9c8fdbcbfa..000000000000
--- a/app-sci/hmmer/files/Makefile-hmmer-2.2g.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- 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/app-sci/hmmer/files/digest-hmmer-2.3.2 b/app-sci/hmmer/files/digest-hmmer-2.3.2
deleted file mode 100644
index a923f14534a4..000000000000
--- a/app-sci/hmmer/files/digest-hmmer-2.3.2
+++ /dev/null
@@ -1 +0,0 @@
-MD5 5f073340c0cf761288f961a73821228a hmmer-2.3.2.tar.gz 1024933
diff --git a/app-sci/hmmer/hmmer-2.3.2.ebuild b/app-sci/hmmer/hmmer-2.3.2.ebuild
deleted file mode 100644
index cfc4639c1e9f..000000000000
--- a/app-sci/hmmer/hmmer-2.3.2.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/hmmer/hmmer-2.3.2.ebuild,v 1.4 2004/11/01 01:53:06 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/app-sci/hmmer/metadata.xml b/app-sci/hmmer/metadata.xml
deleted file mode 100644
index 8a4bcd47220d..000000000000
--- a/app-sci/hmmer/metadata.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?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>