Moving to sci-biology/hmmer

diff --git a/app-sci/hmmer/ChangeLog b/app-sci/hmmer/ChangeLog
deleted file mode 100644 (file)
index 6f03969..0000000
--- 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 (file)
index cf27775..0000000
--- 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 (file)
index fe9c8fd..0000000
--- 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 (file)
index a923f14..0000000
--- 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 (file)
index cfc4639..0000000
--- 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 (file)
index 8a4bcd4..0000000
--- 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>