New version added -20040202, bumped -20031103 to stable, removed stale ebuilds

9 files changed, 61 insertions, 96 deletions

diff --git a/app-sci/ncbi-tools/ChangeLog b/app-sci/ncbi-tools/ChangeLog
index c83ca765400b..bff43d0a361b 100644
--- a/app-sci/ncbi-tools/ChangeLog
+++ b/app-sci/ncbi-tools/ChangeLog
@@ -1,6 +1,20 @@
 # ChangeLog for app-sci/ncbi-tools
 # Copyright 2000-2004 Gentoo Technologies, Inc.; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.6 2004/01/11 13:51:29 lanius Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.7 2004/02/06 00:44:36 sediener Exp $
+
+*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,
diff --git a/app-sci/ncbi-tools/Manifest b/app-sci/ncbi-tools/Manifest
index a9bf4ab421f1..56072ac98686 100644
--- a/app-sci/ncbi-tools/Manifest
+++ b/app-sci/ncbi-tools/Manifest
@@ -3,6 +3,7 @@ MD5 8193311f8812420cc8dd11ff4b6d064f ncbi-tools-04222003.ebuild 2125
 MD5 5494c99330aedd33dbb8b2768805e7cc ncbi-tools-20030422.ebuild 2326
 MD5 60fac9aa207182410d1fa4c26e2aa13a ncbi-tools-04222003-r2.ebuild 2354
 MD5 41fea5bbb2eb97f17b1bb05ed88127ed ncbi-tools-20031103.ebuild 2310
+MD5 c57dda441f2aa6d03d7a578da0e581e0 ncbi-tools-20040202.ebuild 2358
 MD5 50f3512ef67fe22bb637e0936ef2dff2 ChangeLog 1476
 MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
 MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003 114
@@ -11,4 +12,5 @@ MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003-r1 114
 MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003-r2 114
 MD5 cf1401b1b46a3c2c8c6c8ae86d9fd46b files/digest-ncbi-tools-20030422 149
 MD5 45e683cb2a8a9aeaddd120d1ecad032f files/digest-ncbi-tools-20031103 149
+MD5 d9724478c3217255d188863eebeed557 files/digest-ncbi-tools-20040202 140
 MD5 a3e32aea6e4015a69b50f7579e4f3c8e files/21ncbi 140
diff --git a/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003 b/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003
deleted file mode 100644
index 906826ee86d2..000000000000
--- a/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 96208e10f92b2163f5dcc3c5cf74dd44 ncbi.tar.gz 10164179
-MD5 8db14fb4c337372c40140b5cff06b9b6 data.tar.gz 988677
diff --git a/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003-r1 b/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003-r1
deleted file mode 100644
index 906826ee86d2..000000000000
--- a/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003-r1
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 96208e10f92b2163f5dcc3c5cf74dd44 ncbi.tar.gz 10164179
-MD5 8db14fb4c337372c40140b5cff06b9b6 data.tar.gz 988677
diff --git a/app-sci/ncbi-tools/files/digest-ncbi-tools-20040202 b/app-sci/ncbi-tools/files/digest-ncbi-tools-20040202
new file mode 100644
index 000000000000..8cf1e694978a
--- /dev/null
+++ b/app-sci/ncbi-tools/files/digest-ncbi-tools-20040202
@@ -0,0 +1,2 @@
+MD5 365b6e54ea3a4341206c3784348ed39e ncbi-tools-20040202.tar.gz 12987183
+MD5 3403661f9d133187a3040a16b2ab1ed8 ncbi-tools-data.tar.gz 987691
diff --git a/app-sci/ncbi-tools/ncbi-tools-04222003.ebuild b/app-sci/ncbi-tools/ncbi-tools-04222003.ebuild
deleted file mode 100644
index a26aad50f858..000000000000
--- a/app-sci/ncbi-tools/ncbi-tools-04222003.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2003 Gentoo Technologies, Inc.
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-04222003.ebuild,v 1.5 2004/01/13 16:17:08 lanius Exp $
-
-DESCRIPTION="NCBI toolkit including the BLAST group of programs, entrez, ddv, udv, sequin and others"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-
-SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT/ncbi.tar.gz ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT/data.tar.gz"
-
-LICENSE="freedist"
-SLOT="0"
-
-KEYWORDS="x86"
-IUSE="X"
-
-DEPEND="X? ( >=xfree-4.3.0
-	     x11-libs/openmotif )"
-
-S=${WORKDIR}/${P}
-
-src_compile() {
-
-	cd ${WORKDIR}
-	# NCBI provides their own compile script where they check for
-	# the existence of X (openmotif and opengl) libs and compile in support
-	# if they exist
-
-	# future ebuilds will allow for -X which will not compile any of the
-	# graphical tools.  But for right now you get everything if you have
-	# X installed
-
-	./ncbi/make/makedis.csh 2>&1 | tee out.makedis.txt
-
-}
-
-src_install() {
-
-	cd ${WORKDIR}/ncbi/bin
-	dobin Nentrez blastclust entrcmd getmesh megablast testobj Psequin blastpgp entrez2 getpub ncbisort testval asn2ff cdscan errhdr getseq netentcf udv asn2gb checksub fa2htgs gil2bin rpsblast vecscreen asn2xml copymat fastacmd idfetch seedtop asndhuff ddv findspl impala seqtest asntool demo_regexp fmerge indexpub tbl2asn blastall demo_regexp_grep formatdb makemat test_regexp blastcl3 dosimple getfeat makeset testcore
-
-
-	cd ${WORKDIR}
-	dodir /usr/var/ncbi
-	insinto /usr/var/ncbi
-	doins data/*
-
-	dodoc README README.htm VERSION checkout.date
-
-	cd ${WORKDIR}/ncbi/doc
-	dodoc *
-}
-
-pkg_postinst() {
-	einfo "--------------------------"
-	einfo "You must create a .ncbirc file "
-	einfo "for the majority of these programs"
-	einfo "to work right"
-	einfo " "
-	einfo "See README.bls for more information"
-	einfo "--------------------------"
-	einfo "The file should contain the two following lines:"
-	einfo "[NCBI]"
-	einfo "Data=/usr/var/ncbi"
-	einfo "--------------------------"
-	einfo " "
-	einfo "It should be placed in the user's home directory"
-}
diff --git a/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild b/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild
index 17bd8fbb3504..87b3d6e189f1 100644
--- a/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild
+++ b/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2004 Gentoo Technologies, Inc.
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild,v 1.2 2004/01/11 13:51:29 lanius Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild,v 1.3 2004/02/06 00:44:37 sediener Exp $
 
 DESCRIPTION="NCBI toolkit including the BLAST group of programs, entrez, ddv, udv, sequin and others"
 HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
@@ -10,11 +10,15 @@ SRC_URI="mirror://gentoo/ncbi-tools-20030422.tar.gz mirror://gentoo/ncbi-tools-d
 LICENSE="freedist"
 SLOT="0"
 
-KEYWORDS="~x86 ~ppc ~sparc ~alpha"
-IUSE="X"
+KEYWORDS="x86 ~ppc ~sparc ~alpha"
+IUSE="X png"
 
 DEPEND="app-shells/tcsh
-	X? ( >=xfree-4.3.0 x11-libs/openmotif media-libs/libpng )"
+		X? (
+			>=xfree-4.3.0
+			x11-libs/openmotif
+			png? ( media-libs/libpng )
+		)"
 
 S=${WORKDIR}/${P}
 
diff --git a/app-sci/ncbi-tools/ncbi-tools-20031103.ebuild b/app-sci/ncbi-tools/ncbi-tools-20031103.ebuild
index 01ab392cf43c..695c246322d1 100644
--- a/app-sci/ncbi-tools/ncbi-tools-20031103.ebuild
+++ b/app-sci/ncbi-tools/ncbi-tools-20031103.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2004 Gentoo Technologies, Inc.
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-20031103.ebuild,v 1.2 2004/01/11 13:51:29 lanius Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-20031103.ebuild,v 1.3 2004/02/06 00:44:37 sediener Exp $
 
 DESCRIPTION="NCBI toolkit including the BLAST group of programs, entrez, ddv, udv, sequin and others"
 HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
@@ -10,11 +10,15 @@ SRC_URI="mirror://gentoo/${P}.tar.gz mirror://gentoo/${PN}-data-${PV}.tar.gz"
 LICENSE="freedist"
 SLOT="0"
 
-KEYWORDS="~x86 ~ppc ~sparc ~alpha"
-IUSE="X"
+KEYWORDS="x86 ~ppc ~sparc ~alpha"
+IUSE="X png"
 
 DEPEND="app-shells/tcsh
-	X? ( >=xfree-4.3.0 x11-libs/openmotif media-libs/libpng )"
+		X? ( >=xfree-4.3.0
+			x11-libs/openmotif
+			png? ( media-libs/libpng )
+		)"
+
 S=${WORKDIR}/${P}
 
 src_compile() {
diff --git a/app-sci/ncbi-tools/ncbi-tools-04222003-r1.ebuild b/app-sci/ncbi-tools/ncbi-tools-20040202.ebuild
index 98c45ba05fc7..442e75d69068 100644
--- a/app-sci/ncbi-tools/ncbi-tools-04222003-r1.ebuild
+++ b/app-sci/ncbi-tools/ncbi-tools-20040202.ebuild
@@ -1,33 +1,45 @@
 # Copyright 1999-2004 Gentoo Technologies, Inc.
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-04222003-r1.ebuild,v 1.5 2004/01/11 13:51:29 lanius Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-20040202.ebuild,v 1.1 2004/02/06 00:44:37 sediener Exp $
 
 DESCRIPTION="NCBI toolkit including the BLAST group of programs, entrez, ddv, udv, sequin and others"
 HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
 
-SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT/ncbi.tar.gz ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT/data.tar.gz"
+SRC_URI="mirror://gentoo/${P}.tar.gz mirror://gentoo/${PN}-data.tar.gz"
 
 LICENSE="freedist"
 SLOT="0"
 
-KEYWORDS="x86 ~ppc ~sparc ~alpha"
-IUSE="X"
+KEYWORDS="~x86 ~ppc ~sparc ~alpha"
+IUSE="X png"
 
 DEPEND="app-shells/tcsh
-	X? ( >=xfree-4.3.0 x11-libs/openmotif media-libs/libpng )"
+		X? ( >=xfree-4.3.0
+			x11-libs/openmotif
+		 	png? ( media-libs/libpng )
+		)"
 
 S=${WORKDIR}/${P}
 
 src_compile() {
 
 	cd ${WORKDIR}
-	# NCBI provides their own compile script where they check for
-	# the existence of X (openmotif and opengl) libs and compile in support
-	# if they exist
 
-	# future ebuilds will allow for -X which will not compile any of the
-	# graphical tools.  But for right now you get everything if you have
-	# X installed
+	if [ -z "`use X`" ]
+	then
+		ewarn "No X11 apps will be compiled"
+		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" -i ncbi/make/makedis.csh
+		sed -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" -i ncbi/make/makedis.csh
+	fi
+
+	#X11 apps crap out with -O3	
+	sed -e "s:-O3:-O2:g" -i ncbi/platform/linux-x86.ncbi.mk
+	# change to our CFLAGS, use at your own risk
+	# sed -e "s:-pipe:${CFLAGS}:" -i ncbi/platform/linux-x86.ncbi.mk
+	# sed -e "s:-pipe:${CFLAGS}:" -i ncbi/platform/linux.ncbi.mk
+
+	# put in our MAKEOPTS (doesn't work)
+	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
 
 	./ncbi/make/makedis.csh 2>&1 | tee out.makedis.txt
 
@@ -36,7 +48,7 @@ src_compile() {
 src_install() {
 
 	cd ${WORKDIR}/ncbi/bin
-	dobin Nentrez blastclust entrcmd getmesh megablast testobj Psequin blastpgp entrez2 getpub ncbisort testval asn2ff cdscan errhdr getseq netentcf udv asn2gb checksub fa2htgs gil2bin rpsblast vecscreen asn2xml copymat fastacmd idfetch seedtop asndhuff ddv findspl impala seqtest asntool demo_regexp fmerge indexpub tbl2asn blastall demo_regexp_grep formatdb makemat test_regexp blastcl3 dosimple getfeat makeset testcore
+	dobin Nentrez blastclust entrcmd getmesh megablast testobj Psequin blastpgp entrez2 getpub ncbisort testval asn2ff cdscan errhdr getseq netentcf udv asn2gb checksub fa2htgs gil2bin rpsblast vecscreen asn2xml copymat fastacmd idfetch seedtop asndhuff ddv findspl impala seqtest asntool demo_regexp fmerge indexpub tbl2asn blastall demo_regexp_grep formatdb makemat test_regexp blastcl3 dosimple getfeat makeset testcore bl2seq
 
 
 	cd ${WORKDIR}
@@ -44,8 +56,6 @@ src_install() {
 	insinto /usr/var/ncbi
 	doins data/*
 
-	dodoc README README.htm VERSION checkout.date
-
 	cd ${WORKDIR}/ncbi/doc
 	dodoc * images/* fa2htgs/*
 
@@ -62,11 +72,11 @@ src_install() {
 
 pkg_postinst() {
 	einfo " "
-	einfo "You'll need to edit ${FILESDIR}/21ncbi and indicate where your"
+	einfo "You'll need to edit /etc/env.d/21ncbi and indicate where your"
 	einfo "formatdb formatted databases are going to live on the filesystem."
 	einfo "Additionally, you may want to copy /etc/skel/.ncbirc to your"
 	einfo "current users home directories."
 	einfo " "
-	einfo "Be sure to see the ${P} doc directory!"
+	einfo "Be sure to see the /usr/share/doc/${PF} doc directory!"
 	einfo " "
 }