diff options
| -rw-r--r-- | sci-biology/ncbi-tools/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-biology/ncbi-tools/Manifest | 25 | ||||
| -rw-r--r-- | sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 | 9 | ||||
| -rw-r--r-- | sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild | 76 | ||||
| -rw-r--r-- | sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild | 206 |
5 files changed, 280 insertions, 47 deletions
diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog index ed0294c7da36..4a208345ac66 100644 --- a/sci-biology/ncbi-tools/ChangeLog +++ b/sci-biology/ncbi-tools/ChangeLog @@ -1,6 +1,15 @@ # ChangeLog for sci-biology/ncbi-tools # Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.53 2007/06/05 11:00:49 armin76 Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.54 2007/10/13 23:09:17 je_fro Exp $ + + 13 Oct 2007; <jeff@gentoo.org> ncbi-tools-20050605.ebuild, + +ncbi-tools-20070826.ebuild: + Added quotes to make repoman happy. + +*ncbi-tools-20070826 (13 Oct 2007) + + 13 Oct 2007; <jeff@gentoo.org> +ncbi-tools-20070826.ebuild: + New version - mpiblast compilation broken at present. 05 Jun 2007; Raúl Porcel <armin76@gentoo.org> ncbi-tools-20060507.ebuild: alpha stable wrt #152292 diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest index 66e3f0a42cae..c0cded324ba5 100644 --- a/sci-biology/ncbi-tools/Manifest +++ b/sci-biology/ncbi-tools/Manifest @@ -19,14 +19,16 @@ MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33 RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 files/ncbirc 33 SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e files/ncbirc 33 DIST mpiblast-20060625.tar.gz 165096 RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 SHA1 e0acdde2770973b752396a6ba1a99b47ea4ddcde SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 +DIST mpiblast-20070826.tar.gz 286805 RMD160 7c79be86368cf67509c6df124f0ca10deba07d88 SHA1 66233079784b8bc2fcc5dc30f663ecc447163d45 SHA256 0093e55fd21f16f12a39193fe26c685f9fcbd3110c8733f1de0abb8f2a6726f7 DIST ncbi-tools-20050605.tar.gz 14458684 RMD160 82d3c008e9b1741e8ac286d66c1ad68693663590 SHA1 7e1ddd3f049df7c906f2681453c5e5a7b12622d8 SHA256 e0108faeb84da35da82acaa925c084fbeb455c5e571cdcaae5b02c612df46209 DIST ncbi-tools-20060507.tar.gz 15396356 RMD160 56114d25ace0338d1ef5c8c2a3cc36ce740a12e3 SHA1 64269236b09fba29d4afe0cd8a3ac6a47fee5218 SHA256 b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129 DIST ncbi-tools-20061015.tar.gz 15772715 RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 SHA1 4e7990e9fed1cc507d10a1b5285e51dc183d318a SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de +DIST ncbi-tools-20070826.tar.gz 17076175 RMD160 00daadd503bf729c15ada0008e305492a076fe15 SHA1 5e61f4f73ef52d145d0df86bb00f03f2db833ee9 SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8 DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 -EBUILD ncbi-tools-20050605.ebuild 5666 RMD160 8651f586fe414b3b67895467d8b3a89bdcb870d4 SHA1 7732a5d0c3f08a539003877926e2097e9af65320 SHA256 d4a5715743028681d3b3853fdba7e5d9e985cc18c2a198a02e9ebc2cab1e5a75 -MD5 c1ff0f85fcc84dc70c77f129684e5911 ncbi-tools-20050605.ebuild 5666 -RMD160 8651f586fe414b3b67895467d8b3a89bdcb870d4 ncbi-tools-20050605.ebuild 5666 -SHA256 d4a5715743028681d3b3853fdba7e5d9e985cc18c2a198a02e9ebc2cab1e5a75 ncbi-tools-20050605.ebuild 5666 +EBUILD ncbi-tools-20050605.ebuild 5749 RMD160 b44f50468496fd8091515b899d9bc5971db646a3 SHA1 673c0f66d0d2a46b86c5dbcfd2c74d751f531450 SHA256 ff797954513ff7e293ab3519642e0864b781233a7bf15fe5eb98345c8a3c02f5 +MD5 4dd67ba36446b746d08d6a03660409a8 ncbi-tools-20050605.ebuild 5749 +RMD160 b44f50468496fd8091515b899d9bc5971db646a3 ncbi-tools-20050605.ebuild 5749 +SHA256 ff797954513ff7e293ab3519642e0864b781233a7bf15fe5eb98345c8a3c02f5 ncbi-tools-20050605.ebuild 5749 EBUILD ncbi-tools-20060507.ebuild 6406 RMD160 0d52953dc8cff30b92a68fe9a726f19297f7d72d SHA1 4101fa84b7ab60c58ffb42f0b05bd895f5ab6937 SHA256 2653da742470eb3cc79541cdd745af2f858bbd0356ce141b88cc3e1dd07ad9a6 MD5 2f571f2df62cf1f15cee816265ddc847 ncbi-tools-20060507.ebuild 6406 RMD160 0d52953dc8cff30b92a68fe9a726f19297f7d72d ncbi-tools-20060507.ebuild 6406 @@ -35,10 +37,14 @@ EBUILD ncbi-tools-20061015-r1.ebuild 6495 RMD160 24ab84b6a4bce25a0571c78a5489d57 MD5 b87146ee80dd26bf9d65078fafb9bedb ncbi-tools-20061015-r1.ebuild 6495 RMD160 24ab84b6a4bce25a0571c78a5489d5725e81a01b ncbi-tools-20061015-r1.ebuild 6495 SHA256 135d19e95452b5662a9751f4101ef17a66a618c3031894bb2aa8f761d64a85ad ncbi-tools-20061015-r1.ebuild 6495 -MISC ChangeLog 12046 RMD160 f5da07dae177d685279cfc8cb1e808195a324d59 SHA1 2c500e98f4078d01e7e07bb5fbec1b9969b54947 SHA256 9c61bf118f77126decdf8f68383fd4581488e411c23e51e9543487412d5754a2 -MD5 84765ef98775eb5a866921708cff3f5e ChangeLog 12046 -RMD160 f5da07dae177d685279cfc8cb1e808195a324d59 ChangeLog 12046 -SHA256 9c61bf118f77126decdf8f68383fd4581488e411c23e51e9543487412d5754a2 ChangeLog 12046 +EBUILD ncbi-tools-20070826.ebuild 6684 RMD160 181a65b194577401f168d81703749141c4a43fcc SHA1 0d154c687e27a0f49b4b4bf7510a167c5ae1da28 SHA256 8b6967459cb58d7fd8c1938f497e8936392a2350ae3730641c07c0e77084c8ef +MD5 82045b614bc2f6c2dc31416157f92178 ncbi-tools-20070826.ebuild 6684 +RMD160 181a65b194577401f168d81703749141c4a43fcc ncbi-tools-20070826.ebuild 6684 +SHA256 8b6967459cb58d7fd8c1938f497e8936392a2350ae3730641c07c0e77084c8ef ncbi-tools-20070826.ebuild 6684 +MISC ChangeLog 12331 RMD160 f09cf808792211813790563b157a2c480e14dc11 SHA1 e45339d8a5dd0da4e3a2216217ff039489e2f45b SHA256 49dc49e544e0b459b6fa51fc1f90efdd5be3aff58cc7177d3f91a550531bb56b +MD5 37e30369e90d26d20293138270f83b54 ChangeLog 12331 +RMD160 f09cf808792211813790563b157a2c480e14dc11 ChangeLog 12331 +SHA256 49dc49e544e0b459b6fa51fc1f90efdd5be3aff58cc7177d3f91a550531bb56b ChangeLog 12331 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262 @@ -52,3 +58,6 @@ SHA256 d20530e140a48cab2fc12df5a0bf0957e956a6ea35a07b5b5ed42a43466ad4d7 files/di MD5 4a2b24a25719d45c6a999619053cb37c files/digest-ncbi-tools-20061015-r1 777 RMD160 82eefb533a71585a5526c9762f9b389341863252 files/digest-ncbi-tools-20061015-r1 777 SHA256 8dcb338c684c40627c2cfd3a425654b91b29f76804b3c14dde7e4bc4857e3031 files/digest-ncbi-tools-20061015-r1 777 +MD5 cac03cc5ef7883df99f27c9e6ea8e8ec files/digest-ncbi-tools-20070826 777 +RMD160 bd26ddb200c7fca90898c517c8a2f2ecab10f681 files/digest-ncbi-tools-20070826 777 +SHA256 b53edc0b7b44fa711b1abef1d6a4e6d46a36059a7616d7ab5785b66ab622cea5 files/digest-ncbi-tools-20070826 777 diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 new file mode 100644 index 000000000000..591fbdb57d3b --- /dev/null +++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 @@ -0,0 +1,9 @@ +MD5 104239a2c508de944bc68a510b4ca517 mpiblast-20070826.tar.gz 286805 +RMD160 7c79be86368cf67509c6df124f0ca10deba07d88 mpiblast-20070826.tar.gz 286805 +SHA256 0093e55fd21f16f12a39193fe26c685f9fcbd3110c8733f1de0abb8f2a6726f7 mpiblast-20070826.tar.gz 286805 +MD5 c17f7b08c12823e4320661894110dcb1 ncbi-tools-20070826.tar.gz 17076175 +RMD160 00daadd503bf729c15ada0008e305492a076fe15 ncbi-tools-20070826.tar.gz 17076175 +SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8 ncbi-tools-20070826.tar.gz 17076175 +MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568 +RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568 +SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568 diff --git a/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild index be09c595109a..743d24322663 100644 --- a/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild +++ b/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2006 Gentoo Foundation +# Copyright 1999-2007 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild,v 1.13 2006/10/25 19:46:02 grobian Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild,v 1.14 2007/10/13 23:09:17 je_fro Exp $ inherit flag-o-matic toolchain-funcs eutils @@ -36,10 +36,10 @@ pkg_setup() { src_unpack() { unpack ${A} - use ppc64 && cd ${S} && epatch ${FILESDIR}/${PN}-lop.patch + use ppc64 && cd "${S}" && epatch "${FILESDIR}/${PN}-lop.patch" if ! use X; then - cd ${S}/make + cd "${S}/make" sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ -i makedis.csh || die @@ -51,7 +51,7 @@ src_unpack() { fi # Apply user C flags... - cd ${S}/platform + cd "${S}/platform" # ... on x86... sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \ @@ -95,19 +95,19 @@ src_unpack() { } src_compile() { - cd ${WORKDIR} + cd "${WORKDIR}" ncbi/make/makedis.csh || die - mkdir ${S}/cgi - mkdir ${S}/real - mv ${S}/bin/*.cgi ${S}/cgi - mv ${S}/bin/*.REAL ${S}/real + mkdir "${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/* ${D}/usr/include/ncbi + dobin "${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 @@ -117,53 +117,53 @@ src_install() { # 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 ${S}/doc/man/* + dodoc "${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 ${S}/{README.html,doc/{*.html *.gif}} + dohtml "${S}/{README.html,doc/{*.html *.gif}}" insinto /usr/share/doc/${PF}/html/blast - doins ${S}/doc/blast/* + doins "${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} + 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 ${S}/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt} + doins "${S}/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt}" insinto /usr/share/doc/${PF}/regexp/html - doins ${S}/regexp/doc/*.html - doman ${S}/regexp/doc/*.{1,3} + doins "${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/* + 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 ${D}/usr/share/ncbi/demo/regexp/test + mkdir "${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 ${S}/data/* + doins "${S}/data/*" dodir /usr/share/ncbi/formatdb # Default config file to set the path for shared data. insinto /etc/ncbi - newins ${FILESDIR}/ncbirc .ncbirc + newins "${FILESDIR}/ncbirc" .ncbirc # Env file to set the location of the config file and BLAST databases. - newenvd ${FILESDIR}/21ncbi-r1 21ncbi + newenvd "${FILESDIR}/21ncbi-r1" 21ncbi } diff --git a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild new file mode 100644 index 000000000000..2707d0ce1835 --- /dev/null +++ b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild @@ -0,0 +1,206 @@ +# Copyright 1999-2007 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild,v 1.1 2007/10/13 23:09:17 je_fro Exp $ + +inherit flag-o-matic toolchain-funcs eutils autotools + +DESCRIPTION="Development toolkit and applications 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 ) + mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz )" + +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86" + +# IUSE="doc mpi X" +# mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi release. +# Currently seeking a fix. + +IUSE="doc X" + +DEPEND="app-shells/tcsh + dev-lang/perl + media-libs/libpng + sys-devel/pmake + mpi? ( virtual/mpi ) + X? ( virtual/motif )" + +S="${WORKDIR}/ncbi" + +EXTRA_VIB="asn2all asn2asn" + +pkg_setup() { + echo + ewarn 'Please note that the NCBI toolkit (and 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.' + echo +} + +src_unpack() { + unpack ${A} + cd "${S}" + + epatch "${FILESDIR}"/${PN}-extra_vib.patch + + if use ppc64; then + epatch "${FILESDIR}"/${PN}-lop.patch + fi + + if use mpi; then + cd "${WORKDIR}" + epatch "${WORKDIR}"/mpiblast/ncbi_Mar2007_evalue.patch + fi + + if ! use X; then + cd "${S}"/make + sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ + -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ + -i makedis.csh || die + else + if use x86; then + # X applications segfault on startup on x86 with -O3. + replace-flags '-O3' '-O2' + fi + fi + + # Apply user C flags... + cd "${S}"/platform + # ... on x86... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i linux-x86.ncbi.mk || die + # ... on alpha... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \ + -i linux-alpha.ncbi.mk || die + # ... on hppa... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i hppalinux.ncbi.mk || die + # ... on ppc... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i ppclinux.ncbi.mk || die + # ... on generic Linux. + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i linux.ncbi.mk || die + + # 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 = $(tc-getCC)/" linux-x86.ncbi.mk || die + # ... on alpha... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die + # ... on hppa... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die + # ... on ppc... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die + # ... on generic Linux. + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die + + # GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake + # instead. The right solution would be to fix the Makefiles. (Be my guest.) + cd "${S}"/make + sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \ + "Failed to replace make by pmake." +} + +src_compile() { + export EXTRA_VIB + cd "${WORKDIR}" + ncbi/make/makedis.csh || die + mkdir "${S}"/cgi + mkdir "${S}"/real + mv "${S}"/bin/*.cgi "${S}"/cgi || die + mv "${S}"/bin/*.REAL "${S}"/real || die + +# mpiblast fails to compile... perhaps mpiblast2 contain a fix +# if use mpi; then +# cd "${WORKDIR}"/mpiblast +# AM_OPT="-a" +# eautoreconf +# econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die +# emake || die +# fi +} + +src_install() { + dobin "${S}"/bin/* || die "Failed to install binaries." + for i in ${EXTRA_VIB}; do + dobin "${S}"/build/${i} || die "Failed to install binaries." + done + dolib "${S}"/lib/* || die "Failed to install libraries." + mkdir -p "${D}"/usr/include/ncbi + cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \ + die "Failed to install headers." + +# if use mpi; then +# cd "${WORKDIR}"/mpiblast +# make install DESTDIR="${D}" || die "Failed to install MPI blast." +# fi + + # 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}} || \ + die "Failed to install basic documentation." + newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \ + die "Failed renaming fa2htgs documentation." + newdoc "${S}"/config/README README.config || \ + die "Failed renaming config documentation." + newdoc "${S}"/network/encrypt/README README.encrypt || \ + die "Failed renaming encrypt documentation." + newdoc "${S}"/network/nsclilib/readme README.nsclilib || \ + die "Failed renaming nsclilib documentation." + newdoc "${S}"/sequin/README README.sequin || \ + die "Failed renaming sequin documentation." + doman "${S}"/doc/man/* || \ + die "Failed to install man pages." + + # Hypertext user documentation + dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \ + die "Failed to install HTML documentation." + insinto /usr/share/doc/${PF}/html/blast + doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation." + + # Developer documentation + if use doc; then + # Hypertext SDK documentation + insinto /usr/share/doc/${PF}/html/sdk + doins "${WORKDIR}"/${PN}-sdk-doc/* || die + + # Demo programs + mkdir "${D}"/usr/share/ncbi + mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die + fi + + # Shared data (similarity matrices and such) and database directory. + insinto /usr/share/ncbi/data + doins "${S}"/data/* || die "Failed to install shared data." + dodir /usr/share/ncbi/formatdb || die + + # Default config file to set the path for shared data. + insinto /etc/ncbi + newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file." + + # Env file to set the location of the config file and BLAST databases. + newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file." +} |