Moving to sci-biology/ncbi-tools

7 files changed, 0 insertions, 292 deletions

diff --git a/app-sci/ncbi-tools/ChangeLog b/app-sci/ncbi-tools/ChangeLog
deleted file mode 100644
index 51d26ef9e005..000000000000
--- a/app-sci/ncbi-tools/ChangeLog
+++ /dev/null
@@ -1,107 +0,0 @@
-# ChangeLog for app-sci/ncbi-tools
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.19 2004/12/01 05:06:02 j4rg0n Exp $
-
-  30 Nov 2004; <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild:
-  Keyworded ~ppc-macos.
-
-  22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org>
-  ncbi-tools-20040616.ebuild:
-  Added to ~amd64
-
-  14 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20040616.ebuild:
-  Use gcc-getCC from gcc.eclass rather than ${CC}.
-
-  04 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
-  ncbi-tools-20040616.ebuild:
-  Fixed potential bug in "SRC_URI".
-
-*ncbi-tools-20040616 (03 Oct 2004)
-
-  03 Oct 2004; Olivier Fisette <ribosome@gentoo.org> files/21ncbi,
-  -files/dot-ncbirc, +files/ncbirc, -ncbi-tools-20031103.ebuild,
-  -ncbi-tools-20040202-r1.ebuild, +ncbi-tools-20040616.ebuild:
-  Updated version and new ebuild. This fixes bug #65941.
-
-  02 Jun 2004; Aron Griffis <agriffis@gentoo.org> ncbi-tools-20031103.ebuild,
-  ncbi-tools-20040202-r1.ebuild:
-  Fix use invocation
-
-  05 May 2004; Bryan Østergaard <kloeri@gentoo.org>
-  ncbi-tools-20040202-r1.ebuild:
-  Stable on alpha.
-
-  19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org>
-  ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
-  ncbi-tools-20040202.ebuild:
-  Cleanup, removing S=... with no effect
-
-  30 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>;
-  ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
-  ncbi-tools-20040202.ebuild:
-  Change x11-base/xfree dependency to virtual/x11.
-
-  21 Mar 2004; Martin Holzer <mholzer@gentoo.org>
-  ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
-  ncbi-tools-20040202.ebuild:
-  adding categorie. see 45110 for details
-
-*ncbi-tools-20040202-r1 (06 Feb 2004)
-
-  06 Feb 2004; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-20040202-r1.ebuild:
-  Replaced buggy tarball with new one.  Bumped revision to propogate.
-
-*ncbi-tools-20040202 (05 Feb 2004)
-
-  05 Feb 2004; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003.ebuild,
-  ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild,
-  ncbi-tools-20040202.ebuild:
-  Bumped 20031103 to x86, removed old ebuilds, added new release 20040202
-
-*ncbi-tools-20040202 (04 Feb 2004)
-
-  04 Feb 2004; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-20031103.ebuild, ncbi-tools-20040202.ebuild:
-  Version bump.  Changes -O3 -> -O2 so X11 apps will work.
-
-  11 Jan 2004; Heinrich Wendel <lanius@gentoo.org>
-  ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003-r2.ebuild,
-  ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild:
-  fixed motif dep
-
-*ncbi-tools-20031103 (13 Dec 2003)
-
-  13 Dec 2003; Stephen Diener <sediener@gentoo.org>
-  ncbi-tools-20031103.ebuild:
-  Added november release of ncbi-tools (blast-2.2.6 included);
-  Added support for -X
-
-*ncbi-tools-20030422 (11 Nov 2003)
-
-  11 Nov 2003; <sediener@gentoo.org> ncbi-tools-20030422.ebuild:
-  added bl2seq to list of installed binaries; changed date format from 04222003
-  to 20030422; renamed files to have date appended to not collide and changed
-  SRC_URI to mirror://gentoo/
-
-*ncbi-tools-04222003-r2 (08 Oct 2003)
-
-  08 Oct 2003; Robin H. Johnson <robbat2@gentoo.org>
-  ncbi-tools-04222003-r2.ebuild:
-  modified patch from #30656, corrected two pathes in the postinst message
-
-*ncbi-tools-04222003-r1 (05 May 2003)
-
-  05 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003-r1.ebuild :
-  A few enhancements from Gontran Zepeda <gontran@gontran.net>.
-
-*ncbi-tools-04222003 (03 May 2003)
-
-  03 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003 :
-  Initial important. Ebuild submitted by Steve Diener 
-  <sediener@unity.ncsu.edu>.
diff --git a/app-sci/ncbi-tools/Manifest b/app-sci/ncbi-tools/Manifest
deleted file mode 100644
index 7e37e196cf22..000000000000
--- a/app-sci/ncbi-tools/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-MD5 711756bb6acda9b48164aa797e3c2370 ChangeLog 3905
-MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
-MD5 ced23c4353182c6dbac034f001ae951a ncbi-tools-20040616.ebuild 5771
-MD5 756db6700c84d3b303bfc3d0a28871de files/21ncbi 166
-MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
-MD5 6e3486cc782a091aa528a3e3f01192fc files/digest-ncbi-tools-20040616 144
diff --git a/app-sci/ncbi-tools/files/21ncbi b/app-sci/ncbi-tools/files/21ncbi
deleted file mode 100644
index 1983fe83de02..000000000000
--- a/app-sci/ncbi-tools/files/21ncbi
+++ /dev/null
@@ -1,4 +0,0 @@
-# Location of the formatdb data sets
-BLASTDB="/usr/share/ncbi/formatdb"
-# Location of the ".ncbi.rc" file which sets the default path for shared data.
-NCBI=/etc/ncbi
diff --git a/app-sci/ncbi-tools/files/digest-ncbi-tools-20040616 b/app-sci/ncbi-tools/files/digest-ncbi-tools-20040616
deleted file mode 100644
index 5b6b30f6e9ba..000000000000
--- a/app-sci/ncbi-tools/files/digest-ncbi-tools-20040616
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 12320f853acb397a14729fb0da0b09df ncbi-tools-20040616.tar.gz 13680457
-MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/app-sci/ncbi-tools/files/ncbirc b/app-sci/ncbi-tools/files/ncbirc
deleted file mode 100644
index 625dc6a04268..000000000000
--- a/app-sci/ncbi-tools/files/ncbirc
+++ /dev/null
@@ -1,2 +0,0 @@
-[NCBI]
-Data=/usr/share/ncbi/data
diff --git a/app-sci/ncbi-tools/metadata.xml b/app-sci/ncbi-tools/metadata.xml
deleted file mode 100644
index 8a4bcd47220d..000000000000
--- a/app-sci/ncbi-tools/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>
diff --git a/app-sci/ncbi-tools/ncbi-tools-20040616.ebuild b/app-sci/ncbi-tools/ncbi-tools-20040616.ebuild
deleted file mode 100644
index 0c4d333cd6ba..000000000000
--- a/app-sci/ncbi-tools/ncbi-tools-20040616.ebuild
+++ /dev/null
@@ -1,165 +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/ncbi-tools/ncbi-tools-20040616.ebuild,v 1.5 2004/12/01 05:06:02 j4rg0n Exp $
-
-inherit flag-o-matic gcc
-
-DESCRIPTION="Development toolkit and applications (BLAST, entrez, ddv, udv, sequin...) for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="mirror://gentoo/${P}.tar.gz
-	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )"
-
-SLOT="0"
-KEYWORDS="~x86 ~ppc ~sparc ~alpha ~amd64 ~ppc-macos"
-IUSE="doc X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	X? ( virtual/x11
-		x11-libs/openmotif
-	)"
-
-S=${WORKDIR}/ncbi
-
-pkg_setup() {
-	echo
-	ewarn 'It is important to note that the NCBI tools (especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled. If you experience difficulties with this'
-	ewarn 'package and use agressive "CFLAGS", lower the "CFLAGS" and try'
-	ewarn 'to install the NCBI tools again.'
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-
-	if ! use X; then
-		cd ${S}/make
-		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" -i makedis.csh
-		sed -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" -i makedis.csh
-	else
-		if use x86; then
-			# X applications segfault on startup on x86 with -O3.
-			replace-flags '-O3' '-O2'
-		fi
-	fi
-
-	# Apply user C flags...
-	cd ${S}/platform
-	# ... on x86...
-	sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" linux-x86.ncbi.mk
-	sed -i -e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentiumpro/NCBI_LDFLAGS1 = ${CFLAGS}/" linux-x86.ncbi.mk
-	sed -i -e "s/NCBI_OPTFLAG = -O3 -mcpu=pentiumpro/NCBI_OPTFLAG = ${CFLAGS}/" linux-x86.ncbi.mk
-	# ... on alpha...
-	sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" linux-alpha.ncbi.mk
-	sed -i -e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" linux-alpha.ncbi.mk
-	sed -i -e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" linux-alpha.ncbi.mk
-	# ... on hppa...
-	sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" hppalinux.ncbi.mk
-	sed -i -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" hppalinux.ncbi.mk
-	sed -i -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" hppalinux.ncbi.mk
-	# ... on ppc...
-	sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" ppclinux.ncbi.mk
-	sed -i -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" ppclinux.ncbi.mk
-	sed -i -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" ppclinux.ncbi.mk
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" linux.ncbi.mk
-	sed -i -e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" linux.ncbi.mk
-	sed -i -e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" linux.ncbi.mk
-
-	# Put in our MAKEOPTS (doesn't work).
-	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
-
-	# Set C compiler...
-	# ... on x86...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" linux-x86.ncbi.mk
-	# ... on alpha...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" linux-alpha.ncbi.mk
-	# ... on hppa...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" hppalinux.ncbi.mk
-	# ... on ppc...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" ppclinux.ncbi.mk
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" linux.ncbi.mk
-}
-
-src_compile() {
-	cd ${WORKDIR}
-	ncbi/make/makedis.csh || die
-	mkdir ${S}/cgi
-	mkdir ${S}/real
-	mv ${S}/bin/*.cgi ${S}/cgi
-	mv ${S}/bin/*.REAL ${S}/real
-}
-
-src_install() {
-	dobin ${S}/bin/*
-	dolib ${S}/lib/*
-	mkdir -p ${D}/usr/include/ncbi
-	cp -RL ${S}/include/* ${D}/usr/include/ncbi
-
-	# TODO: Web apps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-	# TODO: Add support for wwwblast.
-
-	# Basic documentation
-	dodoc ${S}/{README,VERSION,doc/{*.txt,README.asn2xml}}
-	newdoc ${S}/doc/fa2htgs/README README.fa2htgs
-	newdoc ${S}/config/README README.config
-	newdoc ${S}/network/encrypt/README README.encrypt
-	newdoc ${S}/network/nsclilib/readme README.nsclilib
-	newdoc ${S}/sequin/README README.sequin
-	doman ${S}/doc/man/*
-
-	# Hypertext user documentation
-	dohtml ${S}/{README.html,doc/{*.html *.gif}}
-	insinto /usr/share/doc/${PF}/html/blast
-	doins ${S}/doc/blast/*
-
-	# Developer documentation
-	if use doc; then
-		# "socks" documentation
-		SOCKS="network/socks/socks.cstc.4.2"
-		insinto /usr/share/doc/${PF}/socks
-		doins ${S}/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects}
-		newins ${S}/${SOCKS}/libident/README README.libident
-		doins ${S}/${SOCKS}/sockd/sockd.conf.sample
-		doman ${S}/${SOCKS}/{doc/*.{1,5,8},libident/ident.3}
-		# "regexp" documentation
-		insinto /usr/share/doc/${PF}/regexp
-		doins ${S}/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt}
-		insinto /usr/share/doc/${PF}/regexp/html
-		doins ${S}/regexp/doc/*.html
-		doman ${S}/regexp/doc/*.{1,3}
-		# Hypertext SDK documentation
-		insinto /usr/share/doc/${PF}/html/sdk
-		doins ${WORKDIR}/${PN}-sdk-doc/*
-		# Demo programs
-		mkdir ${D}/usr/share/ncbi
-		mv ${S}/demo ${D}/usr/share/ncbi/demo
-		mv ${S}/regexp/demo ${D}/usr/share/ncbi/demo/regexp
-		mv ${S}/regexp/test ${D}/usr/share/ncbi/demo/regexp/test
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins ${S}/data/*
-	dodir /usr/share/ncbi/formatdb
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins ${FILESDIR}/ncbirc .ncbirc
-
-	# Env file to set the location of the config file and BLAST databases.
-	dodir /etc/env.d
-	insinto /etc/env.d
-	doins ${FILESDIR}/21ncbi
-}