Updates from Gontran Zepeda

6 files changed, 88 insertions, 3 deletions

diff --git a/app-sci/ncbi-tools/ChangeLog b/app-sci/ncbi-tools/ChangeLog
index 9f1730a38a8a..9e11b6b7e275 100644
--- a/app-sci/ncbi-tools/ChangeLog
+++ b/app-sci/ncbi-tools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for app-sci/ncbi-tools
 # Copyright 2000-2003 Gentoo Technologies, Inc.; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.1 2003/05/04 02:37:49 avenj Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.2 2003/05/05 19:36:21 avenj Exp $
+
+*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)
 
diff --git a/app-sci/ncbi-tools/Manifest b/app-sci/ncbi-tools/Manifest
index 07d5f7b99836..1648021b1bc0 100644
--- a/app-sci/ncbi-tools/Manifest
+++ b/app-sci/ncbi-tools/Manifest
@@ -1,6 +1,6 @@
 MD5 109833db222386d7b9090a7d74915452 ncbi-tools-04222003.ebuild 2171
-MD5 2f61656115e3b3cd2d8bd6d632b7616e ChangeLog 405
-MD5 bae9561f1bc85bd9b556a645a118b715 ncbi-tools-04222003-r1.ebuild 2173
+MD5 603ebf642357bff1c588978d97491e7e ChangeLog 587
+MD5 3ff7b645a618cfcf976de72963c0d834 ncbi-tools-04222003-r1.ebuild 2283
 MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003 114
 MD5 7c726288b5f5fd1f2fafcf08a7ffa267 files/dot-ncbirc 26
 MD5 a3e32aea6e4015a69b50f7579e4f3c8e files/21ncbi 140
diff --git a/app-sci/ncbi-tools/files/21ncbi b/app-sci/ncbi-tools/files/21ncbi
new file mode 100644
index 000000000000..6df890a1e114
--- /dev/null
+++ b/app-sci/ncbi-tools/files/21ncbi
@@ -0,0 +1,4 @@
+# where you keep your formatdb formated data sets
+BLASTDB="/usr/var/ncbi/db"
+# convenient for binary or odd location isntall
+#PATH=/usr/bin
diff --git a/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003-r1 b/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003-r1
new file mode 100644
index 000000000000..906826ee86d2
--- /dev/null
+++ b/app-sci/ncbi-tools/files/digest-ncbi-tools-04222003-r1
@@ -0,0 +1,2 @@
+MD5 96208e10f92b2163f5dcc3c5cf74dd44 ncbi.tar.gz 10164179
+MD5 8db14fb4c337372c40140b5cff06b9b6 data.tar.gz 988677
diff --git a/app-sci/ncbi-tools/files/dot-ncbirc b/app-sci/ncbi-tools/files/dot-ncbirc
new file mode 100644
index 000000000000..91582d498dfd
--- /dev/null
+++ b/app-sci/ncbi-tools/files/dot-ncbirc
@@ -0,0 +1,2 @@
+[NCBI]
+Data=/usr/var/ncbi
diff --git a/app-sci/ncbi-tools/ncbi-tools-04222003-r1.ebuild b/app-sci/ncbi-tools/ncbi-tools-04222003-r1.ebuild
new file mode 100644
index 000000000000..03a722fcc2bb
--- /dev/null
+++ b/app-sci/ncbi-tools/ncbi-tools-04222003-r1.ebuild
@@ -0,0 +1,72 @@
+# 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-r1.ebuild,v 1.1 2003/05/05 19:36:21 avenj 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 ~ppc ~sparc ~alpha"
+IUSE="X"
+
+DEPEND="app-shells/tcsh 
+	X? ( >=xfree-4.3.0 >=x11-libs/openmotif-2.2.2 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
+
+	./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 * 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 ${FILESDIR}/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 " "
+}