Moved from app-sci/ncbi-tools to sci-biology/ncbi-tools.

7 files changed, 298 insertions, 0 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
new file mode 100644
index 000000000000..4f60a9c78472
--- /dev/null
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -0,0 +1,113 @@
+# ChangeLog for app-sci/ncbi-tools
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.1 2004/12/23 18:47:51 ribosome Exp $
+
+*ncbi-tools-20040616 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/21ncbi, +files/ncbirc, +ncbi-tools-20040616.ebuild:
+  Moved from app-sci/ncbi-tools to sci-biology/ncbi-tools.
+
+  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/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
new file mode 100644
index 000000000000..7e37e196cf22
--- /dev/null
+++ b/sci-biology/ncbi-tools/Manifest
@@ -0,0 +1,6 @@
+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/sci-biology/ncbi-tools/files/21ncbi b/sci-biology/ncbi-tools/files/21ncbi
new file mode 100644
index 000000000000..1983fe83de02
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/21ncbi
@@ -0,0 +1,4 @@
+# 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/sci-biology/ncbi-tools/files/digest-ncbi-tools-20040616 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20040616
new file mode 100644
index 000000000000..5b6b30f6e9ba
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20040616
@@ -0,0 +1,2 @@
+MD5 12320f853acb397a14729fb0da0b09df ncbi-tools-20040616.tar.gz 13680457
+MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc
new file mode 100644
index 000000000000..625dc6a04268
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbirc
@@ -0,0 +1,2 @@
+[NCBI]
+Data=/usr/share/ncbi/data
diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml
new file mode 100644
index 000000000000..8a4bcd47220d
--- /dev/null
+++ b/sci-biology/ncbi-tools/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>
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20040616.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20040616.ebuild
new file mode 100644
index 000000000000..facce5e9d1dc
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-20040616.ebuild
@@ -0,0 +1,165 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20040616.ebuild,v 1.1 2004/12/23 18:47:51 ribosome 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
+}