diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/emboss/ChangeLog | 13 | ||||
| -rw-r--r-- | sci-biology/emboss/Manifest | 24 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-4.0.0.ebuild | 39 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.0.1.ebuild | 43 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.1.0-r1.ebuild | 41 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.3.1.ebuild | 123 | ||||
| -rw-r--r-- | sci-biology/emboss/files/6.3.1-unbundle-libs.patch | 600 | ||||
| -rw-r--r-- | sci-biology/emboss/files/emboss-README.Gentoo-2 | 34 | ||||
| -rw-r--r-- | sci-biology/emboss/metadata.xml | 3 |
9 files changed, 856 insertions, 64 deletions
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 7e96b832e72f..3b0859c74147 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,15 @@ # ChangeLog for sci-biology/emboss -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.58 2010/07/18 14:17:56 nixnut Exp $ +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.59 2011/03/09 12:00:38 jlec Exp $ + +*emboss-6.3.1 (09 Mar 2011) + + 09 Mar 2011; Justin Lecher <jlec@gentoo.org> + +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2, + emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild, + +emboss-6.3.1.ebuild, metadata.xml: + Version Bump #335603, Unbundled libs, removed old, fix clash with + /usr/bin/digest, #330507 18 Jul 2010; <nixnut@gentoo.org> emboss-6.0.1.ebuild: ppc stable #325457 diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index ed58910a0ca2..2ec47466ce30 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1,13 +1,27 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX 22emboss 110 RMD160 aa416dbfca66cc7822ed162122addadde2756c66 SHA1 c77b477bfdf0e77de4f29794e4fb2e7592557e48 SHA256 cf3bd3b8d2638a0cd14e57839033d63c855114a0e12883bbc7a5106b0cfc01ad +AUX 6.3.1-unbundle-libs.patch 18988 RMD160 0ecaec78052d8c302717113f4883316db84ba49c SHA1 8d10d947492eea2f338313f3e4c8faabfac747c7 SHA256 1f6170a8f4182792d145fd21b6b23d817ea9f5ea39ba77721947ae67a6b6927d AUX README.Gentoo 1326 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 SHA1 8cf13b8aa23c11f0af2aae06916970bf9d8a441f SHA256 33b517b977cc85824847bd6cf4113489a5554fb014f1a6b1d22d6f80c3487e9f AUX emboss-5.0.0-as-needed.patch 1751 RMD160 f43faab31a3d5afb4b73704ba597de578668ae48 SHA1 a108e5f68af9c14363bc56c849c9143fcb7675ba SHA256 e57a60d911e32f1aea16c079e2fd0910a5f7ed43752ea71094d3f3b7575617d3 AUX emboss-README.Gentoo-1 1474 RMD160 a116b4516cd0d8e0b28734bf1e51f1e0833737c4 SHA1 ec23610137ebddc3fc15976757d2cdebd741f9ec SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd +AUX emboss-README.Gentoo-2 1516 RMD160 bf7727ddf6fbf53fc797dba12181332c9e8e93a0 SHA1 1c531f0c1f52569b1d742ec67cc928cb22970f72 SHA256 47f78101b0759f5c629ebee630c14871f1c579c40336a0666647680bc549914e DIST EMBOSS-4.0.0.tar.gz 17651607 RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 SHA1 784c729f2d2e746339a90048277c9e4f052e036a SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 -EBUILD emboss-4.0.0.ebuild 3029 RMD160 75feb6481643ab0dff9e6eda4d0ebbdabde35e3e SHA1 242ee981c5c82d5f207afcc775e2db8981c0e8a7 SHA256 bb9b632b83e03893f984dbdbdab13e5dae9db5a265a87ee4ae8b02e4c5649b22 -EBUILD emboss-6.0.1.ebuild 3492 RMD160 1c3765a2ca2ad4c8d87e846786f956aa84f52768 SHA1 0360bf2e695e56a311dd7bbf8da170ac78b79fb6 SHA256 3a1112d21beb44932db8f582a802edea73ab037878d3e13dfa2b73633d9a2505 -EBUILD emboss-6.1.0-r1.ebuild 3727 RMD160 38ade3c1103e3f07122692d303a92426782d2950 SHA1 368f1a0a94987efa1dab5cfed6f1f2ecfd21ed2a SHA256 cf6488361a70ceb650334e67f7ebba8e891b5f42cb0edb96352d235af95cbf32 +DIST EMBOSS-6.3.1.tar.gz 23572243 RMD160 5c1e7b82e50a183d6ccb323f6a619f10efb0da1a SHA1 efb2e9c1c9b038432ce6bd81ee4692d5f1dc2f72 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d +EBUILD emboss-4.0.0.ebuild 2947 RMD160 8e3bbc8ba2c9cefb3be4c05a4d312dd74faa2663 SHA1 daf9fe4f48cfb630d6a69458c0f3fcc98dd835a5 SHA256 530886491daaac13c8e666abcef254e24c035c96b08a46ae2740bee7f958a50f +EBUILD emboss-6.0.1.ebuild 3463 RMD160 1af6ab9addb475b9ce46910d052de805008fd715 SHA1 3df3f1533a221b4be59624f5e6524b8313a57276 SHA256 4ce83cb04a28fe3e47cf7b58573abeddd0d9013f1ba73ef9d43c3e7f4a0df862 +EBUILD emboss-6.1.0-r1.ebuild 3697 RMD160 468569e7a9c36c140c2612c4c5a238baf311143f SHA1 cf4e0b24cf12fcbb0b5fd5d4873db2005b0de3e5 SHA256 769b157cb2f31b5f3cde923e4095c9a60bfd9f0094050d2931f3b95977d1589f EBUILD emboss-6.1.0.ebuild 3687 RMD160 699d51ab33cea2b5b5d33605146cc18c8e214f27 SHA1 2c2aee3dc1012ea7c36497b08e5e9bae18278bc0 SHA256 4d2416d208de7f3c9223854ad9c801556ec3bc53892b2dd5ffbea8611d9ba1d8 -MISC ChangeLog 9916 RMD160 66125d28bbfa82801d0dab69ab1d0d832c9c615d SHA1 06f3c1d93ef826d81345bedb7a0c525d00b931d6 SHA256 c1dce714cc93c580b27c36e866ae98b61e1603d957cc1d376e655fdd1edf4073 -MISC metadata.xml 924 RMD160 0012a7f8446b6e3ade6b18e2b015bfb80c546712 SHA1 3d47f955e2c7e10fe71ba427c19cc51000990caf SHA256 9a25a29f9ad98792903c439ad7dd4ec485e44e60e23beaf1fa4c209ea89be49b +EBUILD emboss-6.3.1.ebuild 3590 RMD160 1a2b22d033a123b20029ed961274fd19fafd5fb8 SHA1 3e6d957eb262c5e9d18eba890dffdb0d519ce5d6 SHA256 03aacfc484b0a69d2f717887465f714bfe9d35950689046c9e75adab2af2f733 +MISC ChangeLog 10259 RMD160 881391210152b02e618abcb819971b0204e7460f SHA1 2b6b092158a103193e10982186bb3c7fe4ee3e74 SHA256 b33aed1f1adf7332affba6a6d32b99b486930101532ccb994dbd32d2280a324e +MISC metadata.xml 993 RMD160 3204ba9b28338878f0068a8ab5ca7ac6134ce154 SHA1 1bff78caf4aedfc122f0fb01cea4681cf7f3f62e SHA256 1d85e05e979f1657baffabec8dd148786a0cb2eb6b3c0948068290ff877cee2a +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk13a+wACgkQgAnW8HDreRagYACgmYieg06N1OVN2wVsfwWGn0Ne +tTIAoL8d6iLnSySma+cfJe14OpLl5Ozj +=Izz6 +-----END PGP SIGNATURE----- diff --git a/sci-biology/emboss/emboss-4.0.0.ebuild b/sci-biology/emboss/emboss-4.0.0.ebuild index 45108c0c8d75..73fd33c954f8 100644 --- a/sci-biology/emboss/emboss-4.0.0.ebuild +++ b/sci-biology/emboss/emboss-4.0.0.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.13 2010/06/23 12:03:44 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.14 2011/03/09 12:00:38 jlec Exp $ EAPI=1 @@ -13,12 +13,13 @@ SLOT="0" KEYWORDS="amd64 ppc ppc64 ~sparc x86" IUSE="X png minimal" -DEPEND="X? ( x11-libs/libXt ) +DEPEND=" + X? ( x11-libs/libXt ) png? ( sys-libs/zlib media-libs/libpng - >=media-libs/gd-1.8 - ) + media-libs/gd + ) !minimal? ( sci-biology/primer3 sci-biology/clustalw:1 @@ -28,23 +29,25 @@ DEPEND="X? ( x11-libs/libXt ) RDEPEND="${DEPEND} !sys-devel/cons" -PDEPEND="!minimal? ( +PDEPEND=" + !minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/prints - >=sci-biology/prosite-19.7 - >=sci-biology/rebase-601-r1 + sci-biology/prosite + sci-biology/rebase sci-biology/transfac )" S="${WORKDIR}/EMBOSS-${PV}" src_compile() { - EXTRA_CONF="--includedir=${D}/usr/include/emboss" - ! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" - ! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" + local myconf + myconf="--includedir=${D}/usr/include/emboss" + use X || myconf="${EXTRA_CONF} --without-x" + use png || myconf="${EXTRA_CONF} --without-pngdriver" - econf ${EXTRA_CONF} || die + econf ${myconf} # Do not install the JEMBOSS component (the --without-java configure option # does not work). JEMBOSS will eventually be available as a separate package. sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' \ @@ -67,21 +70,21 @@ src_install() { dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die + # Clashes #330507 + mv "${ED}"/usr/bin/{digest,pepdigest} || die + # Remove useless dummy files from the image. - rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ - || die "Failed to remove dummy files." + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." # Move the provided codon files to a different directory. This will avoid # user confusion and file collisions on case-insensitive file systems (see # bug #115446). This change is documented in "README.Gentoo". - mv "${D}"/usr/share/EMBOSS/data/CODONS \ - "${D}"/usr/share/EMBOSS/data/CODONS.orig || \ + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ die "Failed to move CODON directory." # Move the provided restriction enzyme prototypes file to a different name. # This will avoid file collisions with future versions of rebase that will # install their own enzyme prototypes file (see bug #118832). - mv "${D}"/usr/share/EMBOSS/data/embossre.equ \ - "${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ die "Failed to move enzyme equivalence file." } diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild index 75f955ba1d0c..5173f966ff1b 100644 --- a/sci-biology/emboss/emboss-6.0.1.ebuild +++ b/sci-biology/emboss/emboss-6.0.1.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.0.1.ebuild,v 1.6 2010/07/18 14:17:56 nixnut Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.0.1.ebuild,v 1.7 2011/03/09 12:00:38 jlec Exp $ EAPI=1 @@ -15,26 +15,28 @@ SLOT="0" KEYWORDS="amd64 ppc ppc64 ~sparc x86" IUSE="X png minimal" -DEPEND="X? ( x11-libs/libXt ) +DEPEND=" + X? ( x11-libs/libXt ) png? ( sys-libs/zlib media-libs/libpng media-libs/gd - ) + ) !minimal? ( sci-biology/primer3 - sci-biology/clustalw:1 - )" + sci-biology/clustalw + )" RDEPEND="${DEPEND} !sys-devel/cons" -PDEPEND="!minimal? ( +PDEPEND=" + !minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/prints sci-biology/prosite - >=sci-biology/rebase-707 + sci-biology/rebase sci-biology/transfac )" @@ -45,20 +47,21 @@ src_unpack() { cd "${S}" epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch - local link_string="-lX11"; + local link_string="$(pkg-config --libs x11)" if use png; then - link_string="${link_string} -lgd -lpng" + link_string="${link_string} -lgd $(pkg-config --libs libpng)" fi sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ || die "Failed to patch ajax Makefile" } src_compile() { - EXTRA_CONF="--includedir=${D}/usr/include/emboss" - ! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" - ! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" + local myconf + myconf="--includedir=${D}/usr/include/emboss" + use X || myconf="${EXTRA_CONF} --without-x" + use png || myconf="${EXTRA_CONF} --without-pngdriver" - econf ${EXTRA_CONF} || die + econf ${myconf} # Do not install the JEMBOSS component (the --without-java configure option # does not work). JEMBOSS will eventually be available as a separate package. sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ @@ -89,21 +92,21 @@ src_install() { dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die + # Clashes #330507 + mv "${ED}"/usr/bin/{digest,pepdigest} || die + # Remove useless dummy files from the image. - rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ - || die "Failed to remove dummy files." + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." # Move the provided codon files to a different directory. This will avoid # user confusion and file collisions on case-insensitive file systems (see # bug #115446). This change is documented in "README.Gentoo". - mv "${D}"/usr/share/EMBOSS/data/CODONS \ - "${D}"/usr/share/EMBOSS/data/CODONS.orig || \ + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ die "Failed to move CODON directory." # Move the provided restriction enzyme prototypes file to a different name. # This avoids file collisions with versions of rebase that install their # own enzyme prototypes file (see bug #118832). - mv "${D}"/usr/share/EMBOSS/data/embossre.equ \ - "${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ die "Failed to move enzyme equivalence file." } diff --git a/sci-biology/emboss/emboss-6.1.0-r1.ebuild b/sci-biology/emboss/emboss-6.1.0-r1.ebuild index 8a32a9352ae1..4af8ef3e3142 100644 --- a/sci-biology/emboss/emboss-6.1.0-r1.ebuild +++ b/sci-biology/emboss/emboss-6.1.0-r1.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0-r1.ebuild,v 1.2 2010/06/23 12:03:44 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0-r1.ebuild,v 1.3 2011/03/09 12:00:38 jlec Exp $ EAPI="3" @@ -15,26 +15,28 @@ SLOT="0" KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="X png minimal" -DEPEND="X? ( x11-libs/libXt ) +DEPEND=" + X? ( x11-libs/libXt ) png? ( sys-libs/zlib media-libs/libpng media-libs/gd - ) + ) !minimal? ( sci-biology/primer3 sci-biology/clustalw - )" + )" RDEPEND="${DEPEND} !sys-devel/cons" -PDEPEND="!minimal? ( +PDEPEND=" + !minimal? ( sci-biology/aaindex sci-biology/cutg sci-biology/prints sci-biology/prosite - >=sci-biology/rebase-707 + sci-biology/rebase sci-biology/transfac )" @@ -43,20 +45,21 @@ S="${WORKDIR}/EMBOSS-${PV}" src_prepare() { epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch - local link_string="-lX11"; + local link_string="$(pkg-config --libs x11)" if use png; then - link_string="${link_string} -lgd -lpng" + link_string="${link_string} -lgd $(pkg-config --libs libpng)" fi sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ || die "Failed to patch ajax Makefile" } src_configure() { - EXTRA_CONF="--includedir=${ED}/usr/include/emboss" - ! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" - ! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" + local myconf + myconf="--includedir=${ED}/usr/include/emboss" + use X || myconf="${EXTRA_CONF} --without-x" + use png || myconf="${EXTRA_CONF} --without-pngdriver" - econf ${EXTRA_CONF} || die + econf ${myconf} # Do not install the JEMBOSS component (the --without-java configure option # does not work). JEMBOSS will eventually be available as a separate package. sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ @@ -91,21 +94,21 @@ src_install() { rm "${ED}"/usr/share/EMBOSS/doc/programs/text/frestdist.txt || \ die "Failed to remove duplicated documentation." + # Clashes #330507 + mv "${ED}"/usr/bin/{digest,pepdigest} || die + # Remove useless dummy files from the image. - rm "${ED}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ - || die "Failed to remove dummy files." + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." # Move the provided codon files to a different directory. This will avoid # user confusion and file collisions on case-insensitive file systems (see # bug #115446). This change is documented in "README.Gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS \ - "${ED}"/usr/share/EMBOSS/data/CODONS.orig || \ + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ die "Failed to move CODON directory." # Move the provided restriction enzyme prototypes file to a different name. # This avoids file collisions with versions of rebase that install their # own enzyme prototypes file (see bug #118832). - mv "${ED}"/usr/share/EMBOSS/data/embossre.equ \ - "${ED}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ die "Failed to move enzyme equivalence file." } diff --git a/sci-biology/emboss/emboss-6.3.1.ebuild b/sci-biology/emboss/emboss-6.3.1.ebuild new file mode 100644 index 000000000000..e7f52c4dbb4e --- /dev/null +++ b/sci-biology/emboss/emboss-6.3.1.ebuild @@ -0,0 +1,123 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1.ebuild,v 1.1 2011/03/09 12:00:38 jlec Exp $ + +EAPI="4" + +inherit autotools eutils + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +HOMEPAGE="http://emboss.sourceforge.net/" +SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" +LICENSE="GPL-2 LGPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc +largefile minimal mysql pdf png postgres static-libs X" + +DEPEND=" + dev-libs/expat + dev-libs/libpcre:3 + sci-libs/plplot + sys-libs/zlib + mysql? ( dev-db/mysql ) + pdf? ( media-libs/libharu ) + png? ( + sys-libs/zlib + media-libs/libpng + media-libs/gd + ) + postgres? ( dev-db/postgresql-base ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + ) + X? ( x11-libs/libXt )" +RDEPEND="${DEPEND} + !sys-devel/cons" +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-unbundle-libs.patch + eautoreconf +} + +conf-with() { + # USE with-option Option + if use ${1}; then + echo "--with-${2}=${3}" + else + echo "--without-${2}" + fi +} + +src_configure() { + local myconf + myconf="--includedir=${ED}/usr/include/emboss --enable-systemlibs" + + myconf="${myconf} $(conf-with png pngdriver ${EPREFIX}/usr)" + myconf="${myconf} $(conf-with doc docroot ${EPREFIX}/usr)" + myconf="${myconf} $(conf-with pdf hpdf ${EPREFIX}/usr)" + myconf="${myconf} $(conf-with mysql mysql ${EPREFIX}/usr/bin/mysql_config)" + myconf="${myconf} $(conf-with postgresql postgresql ${EPREFIX}/usr/bin/pg_config)" + + econf \ + $(use_with X x) \ + $(use_enable amd64 64) \ + $(use_enable largefile large) \ + $(use_enable static-libs static) \ + --without-java \ + ${myconf} +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS + sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ + dodoc README.Gentoo + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals + dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs + dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials + dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html + + # Clashes #330507 + mv "${ED}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/emboss/files/6.3.1-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1-unbundle-libs.patch new file mode 100644 index 000000000000..5e463744a739 --- /dev/null +++ b/sci-biology/emboss/files/6.3.1-unbundle-libs.patch @@ -0,0 +1,600 @@ +diff --git a/Makefile.am b/Makefile.am +index 4fe2ed1..7f3a95f 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4 + + AUTOMAKE_OPTIONS = gnits + +-SUBDIRS = plplot ajax nucleus emboss test doc jemboss ++if !ESYSTEMLIBS ++EXTRA_DIRS = plplot ++endif ++ ++if GJEMBOSS ++JEMBOSS_DIR = jemboss ++endif ++ ++SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) ++DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) + + # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" + + # files with nonstandard names in this directory +-EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh ++EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh + + # tar to pick up the other directories + # then remove any CVS subdirectories +diff --git a/README.fixes b/README.fixes +new file mode 100644 +index 0000000..3c56d79 +--- /dev/null ++++ b/README.fixes +@@ -0,0 +1,9 @@ ++The files in this directory are bugfix replacements for files in ++the EMBOSS-6.3.1 distribution. Just drop the replacement files in ++the location shown and redo the 'make install.' ++ ++Fix 1. EMBOSS-6.3.1/configure ++ EMBOSS-6.3.1/m4/mysql.m4 ++ ++21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of ++ hpdf support prevented inclusion of MySQL support. +diff --git a/ajax/Makefile.am b/ajax/Makefile.am +index 4a44f6f..cf27ff8 100644 +--- a/ajax/Makefile.am ++++ b/ajax/Makefile.am +@@ -1,6 +1,6 @@ + ## Process this file with automake to produce Makefile.in + if !ESYSTEMLIBS +-EXTRA_DIRS = expat zlib ++EXTRA_DIRS = pcre expat zlib + endif + +-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd ++SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd +diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am +index 02bcaa7..368ddfe 100644 +--- a/ajax/acd/Makefile.am ++++ b/ajax/acd/Makefile.am +@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/ajax/graphics \ +@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libacd_la_LDFLAGS = $(LINKFLAGS) ++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la +diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am +index da57727..857ca5f 100644 +--- a/ajax/ajaxdb/Makefile.am ++++ b/ajax/ajaxdb/Makefile.am +@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre + endif + + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl + +@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajaxdb_la_LDFLAGS = $(LINKFLAGS) ++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la +diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am +index af27cb0..8fa4a3a 100644 +--- a/ajax/core/Makefile.am ++++ b/ajax/core/Makefile.am +@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_LIBS = -lexpat -lpcre + endif + ++EXTRA_DIST = ajax-pcre-config.h.in ++DISTCLEAN = ajax-pcre-config.h + + INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \ + -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \ +--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES) ++$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS) + + AJAXSRC = ajalign.c ajarr.c ajassert.c \ + ajbase.c ajcall.c ajcod.c \ +@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \ + ajmath.h ajmatrices.h ajmem.h ajmess.h \ + ajnam.h ajnexus.h ajobo.h \ + ajpat.h ajpdb.h ajpdbio.h ajphylo.h \ +-ajrange.h ajreg.h ajreport.h ajresource.h \ ++ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \ + ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \ + ajsort.h ajsql.h ajstr.h ajsys.h \ + ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h +@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajax_la_LDFLAGS = $(LINKFLAGS) ++libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS) +diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in +new file mode 100644 +index 0000000..b09e4e6 +--- /dev/null ++++ b/ajax/core/ajax-pcre-config.h.in +@@ -0,0 +1 @@ ++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE +diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h +index 06793be..659f462 100644 +--- a/ajax/core/ajreg.h ++++ b/ajax/core/ajreg.h +@@ -16,9 +16,14 @@ extern "C" + #define ajreg_h + + #include "ajax.h" ++#include "ajax-pcre-config.h" ++#ifndef AJAX_USE_SYSTEM_PCRE + #include "pcre_config.h" + #include "pcre_internal.h" + #include "pcreposix.h" ++#else ++#include <pcre.h> ++#endif + + #define AJREG_OVECSIZE 30 + +@@ -41,7 +46,11 @@ extern "C" + ******************************************************************************/ + + typedef struct AjSRegexp { ++#ifndef AJAX_USE_SYSTEM_PCRE + real_pcre *pcre; ++#else ++ pcre *pcre; ++#endif + pcre_extra *extra; + int *ovector; + const char* orig; +diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am +index ca33a84..87e51bd 100644 +--- a/ajax/ensembl/Makefile.am ++++ b/ajax/ensembl/Makefile.am +@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre + endif + + +-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \ +--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core ++INCLUDES = $(EXTRA_INCLUDES) \ ++-I$(top_srcdir)/ajax/core + + ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \ + ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \ +@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libensembl_la_LDFLAGS = $(LINKFLAGS) ++libensembl_la_LIBADD = ../core/libajax.la +diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am +index ab45afc..f61c605 100644 +--- a/ajax/graphics/Makefile.am ++++ b/ajax/graphics/Makefile.am +@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM ++EXTRA_LIBS = $(PLPLOT_LIBS) + endif + + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core + + AJAXGSRC = ajgraph.c ajhist.c +@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajaxg_la_LDFLAGS = $(LINKFLAGS) ++libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) +diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c +index 25e75e4..60f2743 100644 +--- a/ajax/graphics/ajgraph.c ++++ b/ajax/graphics/ajgraph.c +@@ -34,10 +34,8 @@ + #include <float.h> + #define AZ 28 + +- + #include "plplotP.h" + +- + static void GraphArray(ajuint numofpoints, + float *x, float *y); + static void GraphArrayGaps(ajuint numofpoints, +@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size) + ** @@ + ******************************************************************************/ + ++#define _GNU_SOURCE ++#include <stdio.h> ++ + static void GraphSetName(const AjPGraph thys, + const AjPStr txt, const char *ext) + { + if(!thys->ready) + { ++#ifdef USE_PLXSFNAM_SHIM ++ char *fullname; ++#endif + ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); ++#ifdef USE_PLXSFNAM_SHIM ++ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext); ++ ajDebug("=g= plsfnam ('%S') instead\n", fullname); ++ plsfnam(fullname); ++ free(fullname); ++#else + plxsfnam(ajStrGetPtr(txt), ext); ++#endif + ajStrAssignS(&graphBasename, txt); + ajStrAssignC(&graphExtension, ext); + if(ajStrGetCharFirst(graphExtension) == '.') +diff --git a/configure.in b/configure.in +index ddb4f81..3f4fe5e 100644 +--- a/configure.in ++++ b/configure.in +@@ -235,15 +235,6 @@ AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_MAKE_SET + +-dnl Intel MacOSX 10.6 puts X11 in a non-standard place +-if test "${with_x}" != "no" ; then +-if test "`uname -a | grep Darwin`"; then +-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` +-if test ${OSXX} '>' '10.4'; then +-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" +-fi +-fi +-fi + + # Checks for header files. + #as# AC_PATH_X +@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove) + #as# select socket sqrt strchr strcspn strdup strerror strpbrk \ + #as# strrchr strspn strstr strtol]) + +-if test "${with_x}" != "no" ; then +-LF_EMBOSS_PATH_XLIB +-fi + + dnl Library checks + AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket") +@@ -316,14 +304,16 @@ CHECK_PNGDRIVER + CHECK_AUTH + CHECK_AMD64 + ++AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes") ++ + AX_LIB_MYSQL + AX_LIB_POSTGRESQL + + CFLAGS="$CFLAGS $MYSQL_CFLAGS" + LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS" + +-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS" +-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS" ++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" ++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS" + + + dnl Check for 'ant' for packaging Jemboss and export result +@@ -443,13 +433,36 @@ fi + + dnl Test if --enable-systemlibs given + have_systemlibs=no ++DEFINE_USE_SYSTEM_PCRE="#undef" + AC_ARG_ENABLE(systemlibs, + AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])) ++AC_MSG_CHECKING(for systemlib usage) + if test "${enable_systemlibs}" = "yes" ; then + have_systemlibs=yes ++ DEFINE_USE_SYSTEM_PCRE="#define" ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++ PKG_CHECK_MODULES([ZLIB], [zlib]) ++else ++ dnl X11 is only used by plplot ++ dnl Intel MacOSX 10.6 puts X11 in a non-standard place ++ if test "${with_x}" != "no" ; then ++ if test "`uname -a | grep Darwin`"; then ++ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` ++ if test ${OSXX} '>' '10.4'; then ++ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" ++ fi ++ fi ++ fi ++ if test "${with_x}" != "no" ; then ++ LF_EMBOSS_PATH_XLIB ++ fi ++ AC_MSG_NOTICE(USING bundled LIBS) + fi + AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") + AC_SUBST(ESYSTEMLIBS) ++AC_SUBST(DEFINE_USE_SYSTEM_PCRE) ++AC_SUBST(PLPLOT_CFLAGS) ++AC_SUBST(PLPLOT_LIBS) + + + +@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS) + + dnl Test if purify exists and if --enable-purify given if so + dnl set "-g" +- + AC_MSG_CHECKING(for purify) + dnl if(purify -version) < /dev/null > /dev/null 2>&1; then + AC_ARG_ENABLE(purify, +@@ -683,6 +695,7 @@ CHECK_THREADS + + + AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ++ajax/core/ajax-pcre-config.h + ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile + ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile + ajax/acd/Makefile +diff --git a/emboss/Makefile.am b/emboss/Makefile.am +index 0820517..a0257b2 100644 +--- a/emboss/Makefile.am ++++ b/emboss/Makefile.am +@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \ + yank + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + +-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = -I$(top_srcdir)/nucleus \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ +- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot ++ -I$(top_srcdir)/ajax/acd + + + aaindexextract_SOURCES = aaindexextract.c +@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c + treetypedisplay_SOURCES = treetypedisplay.c + + if !ESYSTEMLIBS +-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ++EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la + endif + + +@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ + ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ + ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ + $(EXTRA_LDS) \ +- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \ + $(XLIB) + + pkgdata_DATA = emboss.default.template +diff --git a/m4/mysql.m4 b/m4/mysql.m4 +index fe413af..ebea25c 100644 +--- a/m4/mysql.m4 ++++ b/m4/mysql.m4 +@@ -1,4 +1,6 @@ +-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html ++# =========================================================================== ++# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html ++# =========================================================================== + # + # SYNOPSIS + # +@@ -6,19 +8,18 @@ + # + # DESCRIPTION + # +-# This macro provides tests of availability of MySQL client library +-# of particular version or newer. ++# This macro provides tests of availability of MySQL client library of ++# particular version or newer. + # +-# AX_LIB_MYSQL macro takes only one argument which is optional. If +-# there is no required version passed, then macro does not run +-# version test. ++# AX_LIB_MYSQL macro takes only one argument which is optional. If there ++# is no required version passed, then macro does not run version test. + # + # The --with-mysql option takes one of three possible values: + # + # no - do not check for MySQL client library + # +-# yes - do check for MySQL library in standard locations +-# (mysql_config should be in the PATH) ++# yes - do check for MySQL library in standard locations (mysql_config ++# should be in the PATH) + # + # path - complete path to mysql_config utility, use this option if + # mysql_config can't be found in the PATH +@@ -33,27 +34,23 @@ + # + # HAVE_MYSQL + # +-# LAST MODIFICATION ++# LICENSE + # +-# 2006-07-16 +-# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers, +-# which prevents gdb from displaying stack traces. +-# Changed mysql_config --cflags to mysql_config --include ++# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net> + # +-# COPYLEFT +-# +-# Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net> +-# +-# Copying and distribution of this file, with or without +-# modification, are permitted in any medium without royalty provided +-# the copyright notice and this notice are preserved. ++# Copying and distribution of this file, with or without modification, are ++# permitted in any medium without royalty provided the copyright notice ++# and this notice are preserved. This file is offered as-is, without any ++# warranty. ++ ++#serial 12 + + AC_DEFUN([AX_LIB_MYSQL], + [ + AC_ARG_WITH([mysql], +- [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], ++ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], + [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config] +- )], ++ ), + [ + if test "$withval" = "no"; then + want_mysql="no" +@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL], + ], + [want_mysql="yes"] + ) ++ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program]) + + MYSQL_CFLAGS="" + MYSQL_LDFLAGS="" + MYSQL_VERSION="" + + dnl +- dnl Check MySQL libraries (libpq) ++ dnl Check MySQL libraries + dnl + + if test "$want_mysql" = "yes"; then + +- if test -z "$MYSQL_CONFIG" -o test; then +- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no]) ++ if test -z "$MYSQL_CONFIG" ; then ++ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) + fi + + if test "$MYSQL_CONFIG" != "no"; then +@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" + + MYSQL_VERSION=`$MYSQL_CONFIG --version` + +-dnl It isn't enough to just test for mysql_config as Fedora +-dnl provides it in the mysql RPM even though mysql-devel may +-dnl not be installed +- +- EMBCFLAGS=$CFLAGS +- EMBLDFLAGS=$LDFLAGS +- CFLAGS=$MYSQL_CFLAGS +- LDFLAGS=$MYSQL_LDFLAGS +- +- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h> +- #include "mysql.h"]], +- [[mysql_info(NULL)]])], +- [havemysql=yes], +- [havemysql=no]) +- +- CFLAGS=$EMBCFLAGS +- LDFLAGS=$EMBLDFLAGS +- +- if test "$havemysql" = yes; then +- AC_DEFINE([HAVE_MYSQL], [1], +- [Define to 1 if MySQL libraries are available]) +- found_mysql="yes" +- AC_MSG_RESULT([yes]) +- else +- MYSQL_CFLAGS="" +- MYSQL_LDFLAGS="" +- found_mysql="no" +- AC_MSG_RESULT([no]) +- fi ++ found_mysql="yes" ++ AC_MSG_RESULT([yes]) + else + found_mysql="no" + AC_MSG_RESULT([no]) +@@ -170,6 +141,11 @@ dnl not be installed + fi + fi + ++ if test "$found_mysql" = "yes" ; then ++ AC_DEFINE([HAVE_MYSQL], [1], ++ [Define to 1 if MySQL libraries are available]) ++ fi ++ + AC_SUBST([MYSQL_VERSION]) + AC_SUBST([MYSQL_CFLAGS]) + AC_SUBST([MYSQL_LDFLAGS]) +diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am +index c244786..ff301b9 100644 +--- a/nucleus/Makefile.am ++++ b/nucleus/Makefile.am +@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \ + -lezlib -leplplot + else + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + endif + + +-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \ +- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \ ++ -I$(top_srcdir)/ajax \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ +@@ -55,3 +58,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libnucleus_la_LDFLAGS = $(LINKFLAGS) ++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2 new file mode 100644 index 000000000000..72fa3662c9a8 --- /dev/null +++ b/sci-biology/emboss/files/emboss-README.Gentoo-2 @@ -0,0 +1,34 @@ +Administrating EMBOSS on Gentoo systems +======================================= + + +Codon data files location +------------------------- + +The codon data files that are distributed with EMBOSS are installed in the +``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual +``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between +these codon files and those installed with the CUTG database. The names of +these files sometimes vary only by their case. Having both sets of files in +the same directory is also impossible on systems such as MacOSX, where the +root filesystem is case insensitive. If you do not have the CUTG database +installed and want to use the codon files distributed with EMBOSS, you can +symlink the ``CODONS.orig`` directory to ``CODONS``:: + + # cd EPREFIX/usr/share/EMBOSS/data + # ln -s CODONS.orig CODONS + + +Restriction enzymes equivalence file location +--------------------------------------------- + +The restriction enzymes equivalence file distributed with EMBOSS is installed +as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual +``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file +collision with the equivalence file provided by the Rebase database. If you do +not have the Rebase database installed and want to use the equivalence file +distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to +``embossre.equ``:: + + # cd EPREFIX/usr/share/EMBOSS/data + # ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml index b85761d07029..747e4ab37d3e 100644 --- a/sci-biology/emboss/metadata.xml +++ b/sci-biology/emboss/metadata.xml @@ -15,4 +15,7 @@ analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. </longdescription> +<use> + <flag name='largefile'>Support for large files</flag> +</use> </pkgmetadata> |