Replaced buggy tarball with new, fixes tblastx error. rev-bumped to propogate.

4 files changed, 98 insertions, 10 deletions

diff --git a/app-sci/ncbi-tools/ChangeLog b/app-sci/ncbi-tools/ChangeLog
index bff43d0a361b..27edc1c02b4a 100644
--- a/app-sci/ncbi-tools/ChangeLog
+++ b/app-sci/ncbi-tools/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.7 2004/02/06 00:44:36 sediener Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.8 2004/02/07 03:43:23 sediener Exp $
+
+*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)
 
diff --git a/app-sci/ncbi-tools/Manifest b/app-sci/ncbi-tools/Manifest
index 56072ac98686..a9b1c470fe3f 100644
--- a/app-sci/ncbi-tools/Manifest
+++ b/app-sci/ncbi-tools/Manifest
@@ -1,16 +1,14 @@
-MD5 3b9a7641e55ab2a567197f767f9860e3 ncbi-tools-04222003-r1.ebuild 2259
-MD5 8193311f8812420cc8dd11ff4b6d064f ncbi-tools-04222003.ebuild 2125
-MD5 5494c99330aedd33dbb8b2768805e7cc ncbi-tools-20030422.ebuild 2326
+MD5 22d3e30f43f90141aac1d40ab861f5f8 ncbi-tools-20030422.ebuild 2352
 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 95f8e91a2bf21841668411a21ccfa9d3 ncbi-tools-20040202-r1.ebuild 2472
+MD5 b0cccd636a4e116d434623ea0477b437 ncbi-tools-20031103.ebuild 2334
+MD5 95f8e91a2bf21841668411a21ccfa9d3 ncbi-tools-20040202.ebuild 2472
+MD5 edc2adb69e5fc470aced30c7b87d390a ChangeLog 2191
 MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
-MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003 114
 MD5 7c726288b5f5fd1f2fafcf08a7ffa267 files/dot-ncbirc 26
-MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003-r1 114
 MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003-r2 114
+MD5 076a160e6c1184393970d0fd636e7c1c files/digest-ncbi-tools-20040202-r1 140
 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 076a160e6c1184393970d0fd636e7c1c files/digest-ncbi-tools-20040202 140
 MD5 a3e32aea6e4015a69b50f7579e4f3c8e files/21ncbi 140
diff --git a/app-sci/ncbi-tools/files/digest-ncbi-tools-20040202-r1 b/app-sci/ncbi-tools/files/digest-ncbi-tools-20040202-r1
new file mode 100644
index 000000000000..6ce0cd0a512e
--- /dev/null
+++ b/app-sci/ncbi-tools/files/digest-ncbi-tools-20040202-r1
@@ -0,0 +1,2 @@
+MD5 37284ef856ae66d191500d936dd77e61 ncbi-tools-20040202.tar.gz 13025387
+MD5 3403661f9d133187a3040a16b2ab1ed8 ncbi-tools-data.tar.gz 987691
diff --git a/app-sci/ncbi-tools/ncbi-tools-20040202-r1.ebuild b/app-sci/ncbi-tools/ncbi-tools-20040202-r1.ebuild
new file mode 100644
index 000000000000..04a092abd18d
--- /dev/null
+++ b/app-sci/ncbi-tools/ncbi-tools-20040202-r1.ebuild
@@ -0,0 +1,82 @@
+# 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-20040202-r1.ebuild,v 1.1 2004/02/07 03:43:24 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="mirror://gentoo/${P}.tar.gz mirror://gentoo/${PN}-data.tar.gz"
+
+LICENSE="freedist"
+SLOT="0"
+
+KEYWORDS="~x86 ~ppc ~sparc ~alpha"
+IUSE="X png"
+
+DEPEND="app-shells/tcsh
+		X? ( >=xfree-4.3.0
+			x11-libs/openmotif
+		 	png? ( media-libs/libpng )
+		)"
+
+S=${WORKDIR}/${P}
+
+src_compile() {
+
+	cd ${WORKDIR}
+
+	if [ -z "`use X`" ]
+	then
+		ewarn "No X11 apps will be compiled"
+		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" -i ncbi/make/makedis.csh
+		sed -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" -i ncbi/make/makedis.csh
+	fi
+
+	#X11 apps crap out with -O3	
+	sed -e "s:-O3:-O2:g" -i ncbi/platform/linux-x86.ncbi.mk
+	# change to our CFLAGS, use at your own risk
+	# sed -e "s:-pipe:${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
+
+}
+
+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 bl2seq
+
+
+	cd ${WORKDIR}
+	dodir /usr/var/ncbi
+	insinto /usr/var/ncbi
+	doins data/*
+
+	cd ${WORKDIR}/ncbi/doc
+	dodoc * images/* fa2htgs/*
+
+	# ncbirc file
+	dodir /etc/skel
+	insinto /etc/skel
+	newins ${FILESDIR}/dot-ncbirc .ncbirc
+
+	# env file
+	dodir /etc/env.d
+	insinto /etc/env.d
+	doins ${FILESDIR}/21ncbi
+}
+
+pkg_postinst() {
+	einfo " "
+	einfo "You'll need to edit /etc/env.d/21ncbi and indicate where your"
+	einfo "formatdb formatted databases are going to live on the filesystem."
+	einfo "Additionally, you may want to copy /etc/skel/.ncbirc to your"
+	einfo "current users home directories."
+	einfo " "
+	einfo "Be sure to see the /usr/share/doc/${PF} doc directory!"
+	einfo " "
+}