diff options
Diffstat (limited to 'app-sci/ncbi-tools')
| -rw-r--r-- | app-sci/ncbi-tools/ChangeLog | 9 | ||||
| -rw-r--r-- | app-sci/ncbi-tools/Manifest | 4 | ||||
| -rw-r--r-- | app-sci/ncbi-tools/files/digest-ncbi-tools-20030422 | 2 | ||||
| -rw-r--r-- | app-sci/ncbi-tools/ncbi-tools-20030422.ebuild | 75 |
4 files changed, 87 insertions, 3 deletions
diff --git a/app-sci/ncbi-tools/ChangeLog b/app-sci/ncbi-tools/ChangeLog index d986aac36e57..1f549cf24d02 100644 --- a/app-sci/ncbi-tools/ChangeLog +++ b/app-sci/ncbi-tools/ChangeLog @@ -1,6 +1,13 @@ # 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 1.3 2003/10/08 22:08:02 robbat2 Exp $ +# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.4 2003/11/11 15:49:33 sediener Exp $ + +*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) diff --git a/app-sci/ncbi-tools/Manifest b/app-sci/ncbi-tools/Manifest index 90eb8e85ebc2..f9bff3d23e39 100644 --- a/app-sci/ncbi-tools/Manifest +++ b/app-sci/ncbi-tools/Manifest @@ -1,8 +1,8 @@ MD5 c2e8575214b0fc09491707b7a62fbf74 ncbi-tools-04222003-r1.ebuild 2269 MD5 67da8c37fd39a6869fffbaf805c4eab5 ncbi-tools-04222003.ebuild 2126 -MD5 6791c1afcc6a643d5dc35ce449ec404d ncbi-tools-20030422.ebuild 2337 +MD5 dabcf899df868cd13e2fd1a00a0db3c1 ncbi-tools-20030422.ebuild 2336 MD5 5da43ab21b280376d96ac8779bf63b0f ncbi-tools-04222003-r2.ebuild 2363 -MD5 b1150f21006f7854123d7623d0be7852 ChangeLog 1080 +MD5 6bb2f40ebfe37145950cd68416526b57 ChangeLog 1081 MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216 MD5 14127812e393e96ae78632a71f4a9f01 files/digest-ncbi-tools-04222003 114 MD5 7c726288b5f5fd1f2fafcf08a7ffa267 files/dot-ncbirc 26 diff --git a/app-sci/ncbi-tools/files/digest-ncbi-tools-20030422 b/app-sci/ncbi-tools/files/digest-ncbi-tools-20030422 new file mode 100644 index 000000000000..a397052e07a0 --- /dev/null +++ b/app-sci/ncbi-tools/files/digest-ncbi-tools-20030422 @@ -0,0 +1,2 @@ +MD5 96208e10f92b2163f5dcc3c5cf74dd44 ncbi-tools-20030422.tar.gz 10164179 +MD5 8db14fb4c337372c40140b5cff06b9b6 ncbi-tools-data-20030422.tar.gz 988677 diff --git a/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild b/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild new file mode 100644 index 000000000000..4992df2356ff --- /dev/null +++ b/app-sci/ncbi-tools/ncbi-tools-20030422.ebuild @@ -0,0 +1,75 @@ +# 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-20030422.ebuild,v 1.1 2003/11/11 15:49:33 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/ncbi-tools-20030422.tar.gz mirror://gentoo/ncbi-tools-data-20030422.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 ${WORKDIR} + # NCBI provides their own compile script where they check for + # the existence of X (openmotif and opengl) libs and compile in support + # if they exist + + # future ebuilds will allow for -X which will not compile any of the + # graphical tools. But for right now you get everything if you have + # X installed + + # put in our cflags + sed -e "s/-O2/${CFLAGS}/" -i ncbi/platform/linux.ncbi.mk + + ./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/* + + 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 ${FILESDIR}/21ncbi +} + +pkg_postinst() { + einfo " " + einfo "You'll need to edit /etc/env.d/21ncbi and indicate where your" + einfo "formatdb formatted databases are going to live on the filesystem." + einfo "Additionally, you may want to copy /etc/skel/.ncbirc to your" + einfo "current users home directories." + einfo " " + einfo "Be sure to see the /usr/share/doc/${PF} doc directory!" + einfo " " +} |