Fixes psipred detection, python file patches

Package-Manager: portage-2.2.0_alpha59/cvs/Linux x86_64

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 311643ae1b8fd4af4c88a314c1e8635bb1d18df6..cd83b35f88174eca9799ad39bb01cae1c8a88f0b 100644 (file)
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.67 2011/09/05 08:55:32 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.68 2011/09/27 08:26:00 jlec Exp $
+
+*ccpn-2.2.1_p110926 (27 Sep 2011)
+*ccpn-2.1.5_p110926 (27 Sep 2011)
+
+  27 Sep 2011; Justin Lecher <jlec@gentoo.org> +ccpn-2.1.5_p110926.ebuild,
+  +ccpn-2.2.1_p110926.ebuild, files/analysis, files/dangle, files/dataShifter,
+  files/depositionFileImporter, files/eci, files/extendNmr,
+  files/formatConverter, files/pipe2azara, files/xeasy2azara:
+  Fixes psipred detection, python file patches
 
 *ccpn-2.2.1_p110905 (05 Sep 2011)
 *ccpn-2.1.5_p110905 (05 Sep 2011)

diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index b1f9eb4fe30e30e2912378a5a81ad7c97abf7f49..0e28d530445824b194fcfffaac522a3d3c65825a 100644 (file)
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -6,15 +6,15 @@ AUX 2.1.3_1-impl-dec.patch 2818 RMD160 182cb26478750711916c73b7f9ba5e0caeb30bde
 AUX 2.1.3_1-parallel.patch 577 RMD160 8bafa14bec766aaca0e55f33f9b51f10f5f29c43 SHA1 e95891313f669e0908374aa98a725596140150cf SHA256 7e650ef2fa1ff0626349affdf1bc9578fe1da3b8cee7dd9125d33a2164978b69
 AUX 2.1.5-parallel.patch 850 RMD160 8120e0ff579b6ec575cb96b51b8babec63116e0c SHA1 1389f1703ecf86d5ce98a3854314bd85d5c350e1 SHA256 5d9a1a4f1392057167312a844972608fa25afb821453b2057ac1acd03b8711d5
 AUX 2.2.1-parallel.patch 850 RMD160 c2d0c523637325de3109894e564cfdea77e9c11e SHA1 beca108b9d2d17ea550bb26b95fa83160d38eb3a SHA256 318bbf3ae5b04e8cbe0e8e93a7e81a7e793fffa9a0d754464367092d6b79f04d
-AUX analysis 290 RMD160 0615c926527a59cbcafd2084680bd491f55c6295 SHA1 03ed24715a97f96857026ca018c141ad3e685301 SHA256 ce472f49720fe6ed1f217c519ad66eb5921e64e0d4d002683dc516846b99c30d
-AUX dangle 286 RMD160 b0e6b5162b8940f129debfd006fba635b6d250e9 SHA1 d83cf9ee0940ff3d7c62270d8a79384b4e49f7af SHA256 3913f3ea1638638b76997ce02320bde74d279b3391d177e11d11678bfee9da08
-AUX dataShifter 289 RMD160 dde8a9f9effc6ef682cfad550a12b0e98585c8ec SHA1 0ccde2b8aeecdfe5b30c7b953e9cc49f61de3631 SHA256 27daf72a001b8114b7b133a0fb0c284f334a45026f1c1afcd29e46efc794f16d
-AUX depositionFileImporter 293 RMD160 e5dc5bf542652f193a4da5892c87d3d31c1c8dcd SHA1 cb2658e18fde0678522088589148f38dba8a0397 SHA256 d2a31b0ce2218563adcda403d4f1176df9ac7bd68425fb7f5df811e645387454
-AUX eci 274 RMD160 a940e822e64242500ec3aa656f41d908724a3ba2 SHA1 018cd59152dbfb50805e14b7f0df1230c0e6ed68 SHA256 89501b1a5a79d3bcfdd384c8831e42546d861435ac27627e00438227a0e84b59
-AUX extendNmr 273 RMD160 e8558632bd7ed7760af629afcb18b99ed2779995 SHA1 d78727d0900ff2424a0a8317f6d740876abd496f SHA256 2c690613c543498900a5073b0347cd5e43ef9014ab93abefccfdd871415d26d3
-AUX formatConverter 293 RMD160 a2229663a5d682e17af8a6cb5f927f66ce59bea6 SHA1 fcd45ab7019911756194457bef1889b4320f00f5 SHA256 e0a4c8303185813084b3f2077e8909cd72593f1d0043443d7ba5f21901f81d2a
-AUX pipe2azara 297 RMD160 0cd01c0cf629710ff4b4267d9449b0b1f3d586e1 SHA1 16566033682903504d77f4acaa93a6625557087e SHA256 e34774b668732c3f4fb764e6c83cc938da3fb514cf5a58bb820827304dc80979
-AUX xeasy2azara 295 RMD160 1d0ba266c71d25d5afa3df243c84000307787dc3 SHA1 8ccbbd7ac24b9f2ec943899e0df1297d2d614623 SHA256 833ebb5b390e4181d15d7e5d2fc703b82e2dca65d6a90f575645c22ccec68ed9
+AUX analysis 319 RMD160 90f2fadd0c95c6d7d5f38c9a59bb6f72ea610c6a SHA1 7433d87b0eea322a67a3d3dfe71ff3075ebcc864 SHA256 0731b9a1624259b373c7163c6ad095c82f77965f0b61880e84bc8e3c30b83d6e
+AUX dangle 315 RMD160 5e0e4a03ecf427687157677e2fd64316312fefc7 SHA1 570799f08e63e32bf3767b755de82ce691a5bafb SHA256 03101ba39fc9fef1380315c2c64f9d027fb95b79d82c35b9971445613ad5774d
+AUX dataShifter 318 RMD160 c9054be6091ace5e80aef1fb2a226c5658d16ee3 SHA1 8144ab11963c25bb6f57e8a91efa31a35e0c85f8 SHA256 891f87e2eaae88253ffddd4e71b060f8b8e7711d54a02492117500186f04f45d
+AUX depositionFileImporter 322 RMD160 4d93874079c06c14a9fdb4c5411aff2288c7be98 SHA1 e6a8232468a83acb63aa6422279693418dd21fce SHA256 ba96561ccef577126df3454b0ef2207e6fe32ecb178e98bc0e106423553e0f33
+AUX eci 303 RMD160 b1857ee3ec7e24d94efed7091ee7fbd8a0afbc69 SHA1 abdb2ff45b5d2e46b38d3459b12882a2c29e39b4 SHA256 e54ccd50ae69d94ba3f72c347b974e1b878bd63e28fd4c43a6b095e187daf791
+AUX extendNmr 302 RMD160 3268bddbe371846fae3b6ee71aa17b38345c1aaa SHA1 72c35915799db4c73c6d1d5463663da37f6b94f2 SHA256 4c483a09abf5fa3043a51dda55e7f528faecbf56769a3306f397b3848137cee6
+AUX formatConverter 322 RMD160 acd331ab2ca211eb06c4e4e3263b6c000a4d2cdb SHA1 5b5b14bfcd8cdf375075de214139f1fceca42747 SHA256 86b2613d7842ee3777fd98889abe6450266140d6fe6ed7d071db6b549c2afb65
+AUX pipe2azara 326 RMD160 debd9e9aa96265858bcf29618b9790954deacf9e SHA1 b0e153d904014fa84c1b399bf64ae594316b4608 SHA256 8b17d8c11dcbfeac21da3ad927e2e8de73509d21e9250c328fbea1aba658611c
+AUX xeasy2azara 324 RMD160 88b4967ef4822ff04264f2b632a1dbfca3fe23f0 SHA1 1c877d6e01258575ae1066045ca0e621cf8fcb33 SHA256 89945dae1c7bd78aefdd19c81c79571a13aaa149d6c50e12cc0ecd075930ed4c
 DIST analysis2.1.3_1.tar.gz 18932918 RMD160 5f19ea6fe47c2910d16fcba8d1a78f0e1dead731 SHA1 683bdfb17d14979eb6477aaa99e4c4af5003beb2 SHA256 bbc1ba5434f896d38b6745c1dc9adc470a78d3be7b879160edcd635a19228b74
 DIST analysis2.1.5.tar.gz 20338459 RMD160 b0706c859c1ee4da2ab80ee41534197268f73d44 SHA1 70dc5e6b2752d6b7d5c8673fc992ebd0a88e6ad0 SHA256 9f91f1bd56fb73fd24e71d396c96c0f0d31b92287664b6a2e756f6efc630b31b
 DIST analysis2.2.1.tar.gz 20974926 RMD160 5905f43fc1399a656f018808c4a2f8dd3d247ca9 SHA1 eed30da55a719ef6c29431e3b3c5a76f521010dc SHA256 d1252811b3db3a30d96a73368bae8abcb05de02fcd2f1f9c502d71dff5e00d13
@@ -23,25 +23,29 @@ DIST ccpn-update-2.1.5-110602.patch.bz2 81505 RMD160 2af0d5ca21828ccc3345ec763ed
 DIST ccpn-update-2.1.5-110629.patch.bz2 86224 RMD160 d4cb190ce84f62639d77f6592475746e8b9f6a0e SHA1 e20f3313853dff4a3de723a2efc70efe81c63861 SHA256 df847050c95ea925db16a5c6630861e308d39286cc7c207efc4360fce53e29b2
 DIST ccpn-update-2.1.5-110817.patch.bz2 88191 RMD160 9fe24e51a1416cdde25ac6d25c2764840c1a00ef SHA1 d16956e6ad7530d17c9e46b877eaf993959f49a2 SHA256 176fd4488c40d7eb426df353d85a05ddb8e4b4126f32264c9d536bf1799fe44c
 DIST ccpn-update-2.1.5-110905.patch.bz2 99670 RMD160 d3163c0d2d07661e318fa101267ef9dba6d05244 SHA1 3b61f72e66bf56c8c2799b864eef91643a30f367 SHA256 c2fa8f6c3f9826747e9f244a46b7ab701ff83dabc36f8ae534db0d76239c5da9
+DIST ccpn-update-2.1.5-110926.patch.bz2 99882 RMD160 8e1aa7563ea395c9ef68c87fb4d400d8d8ddc3ec SHA1 efafa90ae1edd7bf0be0bffad76c27c514b47213 SHA256 cff2cec1728fa92636ec4b89d638238755ae055c12b8453298c3ee9daceac012
 DIST ccpn-update-2.2.1-110602.patch.bz2 57084 RMD160 502c9ca948caf7be5e87759222982a952dd81bc2 SHA1 31725499eba0bb851357227fc4db274121a32240 SHA256 591be1c0c5dfea56c7fa8aec5da154a2a7263a11e8e20ff2a71a2e6e484c6e00
 DIST ccpn-update-2.2.1-110629.patch.bz2 66050 RMD160 8d3b37d9c848f177b4c35f36eccd1026500af0b4 SHA1 66371f52b15ec8c689c1634fa30f6679c4e8c681 SHA256 99280022b594a45d1bdb9811f0f78851a8cb8282476c521987def7ab13cb0dac
 DIST ccpn-update-2.2.1-110817.patch.bz2 77149 RMD160 69c2417ca700129d9c53f90d5be665b2192ae0c0 SHA1 b61874c4753251ac08fd4549f6b656352e462ece SHA256 f08b1082435546c605d516167617cdf5b163aa820150718fa8e205cd4f9a3232
 DIST ccpn-update-2.2.1-110905.patch.bz2 78329 RMD160 295a3057f4ccd0ad89a3bc75a9992351953be891 SHA1 b7f1e545777d5850564475ce5fb495c0f516a748 SHA256 e3823d29f58a2f6adb3a1855c6665604d8cff8a7f26af75f2b8c6c990a58a36f
+DIST ccpn-update-2.2.1-110926.patch.bz2 79805 RMD160 2eb19fe8cc1bcf98dba2aa892f41cef16ababd01 SHA1 09199cec4c733befb32558d5138fff93a94fa03f SHA256 5e8b44399cb0fd3b0a20405c3c65428aefd3a47445a003e40f4caac2fe77fd41
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5188 RMD160 b66825e37b79a5f6ec6635b9f3236d1cda2da672 SHA1 458f516ffad25d9283b21c9dfb8e50c6323f4264 SHA256 ff57abefefd3bb128a3f96bf039cbaa5ed97350f6b41fdbdd4b4365ff9e68e51
 EBUILD ccpn-2.1.5_p110602.ebuild 5794 RMD160 8a28dce36877c1bf37a188364d831322f6a88049 SHA1 a5bbc2015b8b7f7f8a11e9a6297be2f80edcf585 SHA256 6c28d2dfd433267d1dcd5ba25de0ae6a8dcfd312df2943cca70e2eb896b2343b
 EBUILD ccpn-2.1.5_p110629.ebuild 5794 RMD160 a4bc4bfc58ac834cb2551366e8eaf59eb9079f6f SHA1 679454b9f8f7317ebb4b75d9729efe2ccd8fcd1e SHA256 4eb9b69f024bf309d9f88468528aeecffa03f14e96d59a5fca3ce8733e7f6bf0
 EBUILD ccpn-2.1.5_p110817.ebuild 5794 RMD160 d18b5e31dcb31eeaff5dc88a26ce2e5db7147906 SHA1 f2485d1ba0d0a7110b1947019770e045e43f8e2c SHA256 8c8a13a96ea4b5707879a422245117491ca4b87f46b3aa2a63e74379ffcc5de1
 EBUILD ccpn-2.1.5_p110905.ebuild 5794 RMD160 5b40785ae8c0471b54e19fa04f0ed008a50f1aa5 SHA1 a728c6529fb566c5537dd6e8c4c0fc75d5725bef SHA256 e009253f4bc3c8b50af8a036a457ec81cb70e06cdd2156e8d8a336acc8e8b16a
+EBUILD ccpn-2.1.5_p110926.ebuild 5971 RMD160 632413ffb550cfc36299c2107b430c4eb3ae3bdf SHA1 5e6c3fa4d68ee075c785d4101740f36698bc9098 SHA256 4891223c20b5be543e892f746dc59d5b4d2dd34b45f492e0593852bbda103197
 EBUILD ccpn-2.2.1_p110602.ebuild 5806 RMD160 ad1b5507ba8c6534023cf02498a1689ebad49b71 SHA1 18935d2bb4af71fd0063927084d5bb1a454672dc SHA256 e5d6eae560e472bfa730454d37dad7d7979ded74a2fa7bbcec963332d68d7c0d
 EBUILD ccpn-2.2.1_p110629.ebuild 5806 RMD160 a63bf6ce2b38cfb5a39a1b98a0666d492fd90c87 SHA1 695710527df0138d62a448870e0a3809aab1ccae SHA256 fad2ae44188fa8fd22f1d0096c9d2164ea947e57f170683e08781fb7f1364f60
 EBUILD ccpn-2.2.1_p110817.ebuild 5806 RMD160 397603fb9fea25aea0c5a9d92029a535e2ae7aa2 SHA1 376860302c8aab8fc0a3bcd33931eff158c4459a SHA256 ae98ca1bd9383d1d16051f66e9056bb37884261514e6aec469dfb2a9ebaeb318
 EBUILD ccpn-2.2.1_p110905.ebuild 5806 RMD160 12307b04226e935f4b81649515a0cfbfc6d1b26c SHA1 fe299ba1ab0dbe330dbe3170e74d0488943291ae SHA256 e770d80a032174cdd5e533afd5d70caa8e8913e44544eb151c02334ef770480f
-MISC ChangeLog 12359 RMD160 004b2b8a2a967e2ffe9dacef917363a6c25385f8 SHA1 2821106f79a555127d0d1d09a16f4f3281a016ac SHA256 f4a0835b7fef3737634e614d8aa08d2d66062e9da212d41e34379974819d9588
+EBUILD ccpn-2.2.1_p110926.ebuild 5983 RMD160 3a1f53b1e71cb58c3d8668ef73bd4a13bb70c19c SHA1 cae4a96243081a557393fe8c522f67539bfcec29 SHA256 070cb02b41dc1361a82c8450d120de472639114bf0059c1b83d17ddf78814e19
+MISC ChangeLog 12752 RMD160 951407cfb564668298cd89e1c20cbb84bb07bc33 SHA1 d706bc8741dad3f10e00869facb3bc276e559b61 SHA256 522c3a07ccca5ca8c737e9d2f9e3397dde5631340abf0c12aa185b0b9ac237e9
 MISC metadata.xml 322 RMD160 9fd5fba7405b689fc39a089d81ffdaa9f961b514 SHA1 0c31132b25fca04cff97ef11fdc11940f90c77d0 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.18 (GNU/Linux)
 
-iEYEAREKAAYFAk5kjooACgkQgAnW8HDreRa4fQCgm4UbmuQFUokV8ddXQUE3ESmr
-fOMAn0SPhD1ywtcEMlKAfkFS21F6uGtC
-=G2da
+iEYEAREKAAYFAk6BiL4ACgkQgAnW8HDreRZzRACeIcqVrWxRzLa3KNC05o6eDTjW
+kvwAniYuqZUtiwxTpHfmV6L2yJUeeRUh
+=tocu
 -----END PGP SIGNATURE-----

diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild
new file mode 100644 (file)
index 0000000..2042c46
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild
@@ -0,0 +1,219 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild,v 1.1 2011/09/27 08:26:00 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.5"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python toolchain-funcs versionator
+
+PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+       [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}     http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="extendnmr +opengl"
+
+RDEPEND="
+       dev-lang/tk[threads]
+       >=dev-python/numpy-1.4
+       >=dev-tcltk/tix-8.4.3
+       =sci-libs/ccpn-data-"${MY_MAJOR}"*
+       sci-biology/psipred
+       x11-libs/libXext
+       x11-libs/libX11
+       opengl? (
+               media-libs/freeglut
+               dev-python/pyglet )"
+# We need to fix this
+#              sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+       extendnmr? (
+               sci-chemistry/aria
+               sci-chemistry/prodecomp )"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+       python_set_active_version 2
+}
+
+src_prepare() {
+       [[ -n ${PATCHSET} ]] && \
+               epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+       epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+       sed \
+               -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+               -i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+       local tk_ver
+       local myconf
+
+       tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+       if use opengl; then
+               GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+               IGNORE_GL_FLAG=""
+               GL_FLAG="-DUSE_GL_TRUE"
+               GL_DIR="${EPREFIX}/usr"
+               GL_LIB="-lglut -lGLU -lGL"
+               GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+               GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+       else
+               IGNORE_GL_FLAG="-DIGNORE_GL"
+               GL_FLAG="-DUSE_GL_FALSE"
+       fi
+
+       GLUT_NOT_IN_GL=""
+       GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+       rm -rf data model doc license || die
+
+       sed \
+               -e "s|/usr|${EPREFIX}/usr|g" \
+               -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+               -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
+               -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
+               -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
+               -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
+               -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
+               -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
+               -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
+               -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
+               -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
+               -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
+               -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+               -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+               -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+               -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
+               -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
+               c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+       emake -C c all links || die
+}
+
+src_install() {
+       local libdir
+       local tkver
+       local _wrapper
+
+       find . -name "*.pyc" -type d -delete
+
+       libdir=$(get_libdir)
+       tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+       _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
+       use extendnmr && _wrapper="${_wrapper} extendNmr"
+       for wrapper in ${_wrapper}; do
+               sed \
+                       -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+                  -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+                       -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+                       -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+                       -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
+                       -e "s|gentoousr|${EPREFIX}/usr|g" \
+                       -e "s|//|/|g" \
+                       "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+               dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+       done
+
+       local in_path
+       local files
+       local pydocs
+
+       pydocs="$(find python -name doc -type d)"
+       rm -rf ${pydocs} || die
+
+       in_path=$(python_get_sitedir)/${PN}
+
+       for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+       sed \
+               -e 's|#from __future__|from __future__|g' \
+               -i ${i} || die
+       done
+
+       insinto ${in_path}
+
+       dodir ${in_path}/c
+
+       ebegin "Installing main files"
+               doins -r python || die "main files installation failed"
+       eend
+               dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
+       for i in ${pydocs}; do
+               dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
+       done
+
+       dosym /usr/share/ccpn/data ${in_path}/data
+       dosym /usr/share/ccpn/model ${in_path}/model
+
+       einfo "Adjusting permissions"
+
+       files="
+               cambridge/c/BayesPeakSeparator.so
+               ccp/c/StructUtil.so
+               ccp/c/StructStructure.so
+               ccp/c/StructBond.so
+               ccp/c/StructAtom.so
+               ccpnmr/c/DyAtomCoord.so
+               ccpnmr/c/DyDistConstraint.so
+               ccpnmr/c/DyDistForce.so
+               ccpnmr/c/AtomCoordList.so
+               ccpnmr/c/DyAtomCoordList.so
+               ccpnmr/c/ContourStyle.so
+               ccpnmr/c/ContourLevels.so
+               ccpnmr/c/SliceFile.so
+               ccpnmr/c/PeakCluster.so
+               ccpnmr/c/Dynamics.so
+               ccpnmr/c/Bacus.so
+               ccpnmr/c/Midge.so
+               ccpnmr/c/DyDistConstraintList.so
+               ccpnmr/c/WinPeakList.so
+               ccpnmr/c/PeakList.so
+               ccpnmr/c/DistConstraint.so
+               ccpnmr/c/CloudUtil.so
+               ccpnmr/c/DistForce.so
+               ccpnmr/c/DistConstraintList.so
+               ccpnmr/c/AtomCoord.so
+               ccpnmr/c/DyDynamics.so
+               ccpnmr/c/ContourFile.so
+               memops/c/ShapeFile.so
+               memops/c/BlockFile.so
+               memops/c/PdfHandler.so
+               memops/c/MemCache.so
+               memops/c/FitMethod.so
+               memops/c/PsHandler.so
+               memops/c/GlHandler.so
+               memops/c/StoreFile.so
+               memops/c/StoreHandler.so
+               memops/c/TkHandler.so"
+       for FILE in ${files}; do
+               fperms 755 ${in_path}/python/${FILE}
+       done
+}
+
+pkg_postinst() {
+       python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+       python_mod_cleanup ${PN}
+}

diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild
new file mode 100644 (file)
index 0000000..db42bdd
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild
@@ -0,0 +1,219 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild,v 1.1 2011/09/27 08:26:00 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.5"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python toolchain-funcs versionator
+
+PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+       [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}     http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="extendnmr +opengl"
+
+RDEPEND="
+       dev-lang/tk[threads]
+       >=dev-python/numpy-1.4
+       >=dev-tcltk/tix-8.4.3
+       =sci-libs/ccpn-data-"${MY_MAJOR}"*
+       sci-biology/psipred
+       x11-libs/libXext
+       x11-libs/libX11
+       opengl? (
+               media-libs/freeglut
+               dev-python/pyglet )"
+# We need to fix this
+#              sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+       extendnmr? (
+               sci-chemistry/aria
+               sci-chemistry/prodecomp )"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+       python_set_active_version 2
+}
+
+src_prepare() {
+       [[ -n ${PATCHSET} ]] && \
+               epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+       epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+       sed \
+               -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+               -i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+       local tk_ver
+       local myconf
+
+       tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+       if use opengl; then
+               GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+               IGNORE_GL_FLAG=""
+               GL_FLAG="-DUSE_GL_TRUE"
+               GL_DIR="${EPREFIX}/usr"
+               GL_LIB="-lglut -lGLU -lGL"
+               GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+               GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+       else
+               IGNORE_GL_FLAG="-DIGNORE_GL"
+               GL_FLAG="-DUSE_GL_FALSE"
+       fi
+
+       GLUT_NOT_IN_GL=""
+       GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+       rm -rf data model doc license || die
+
+       sed \
+               -e "s|/usr|${EPREFIX}/usr|g" \
+               -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+               -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
+               -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
+               -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
+               -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
+               -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
+               -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
+               -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
+               -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
+               -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
+               -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
+               -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+               -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+               -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+               -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
+               -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
+               c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+       emake -C c all links || die
+}
+
+src_install() {
+       local libdir
+       local tkver
+       local _wrapper
+
+       find . -name "*.pyc" -type d -delete
+
+       libdir=$(get_libdir)
+       tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+       _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
+       use extendnmr && _wrapper="${_wrapper} extendNmr"
+       for wrapper in ${_wrapper}; do
+               sed \
+                       -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+                  -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+                       -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+                       -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+                       -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
+                       -e "s|gentoousr|${EPREFIX}/usr|g" \
+                       -e "s|//|/|g" \
+                       "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+               dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+       done
+
+       local in_path
+       local files
+       local pydocs
+
+       pydocs="$(find python -name doc -type d)"
+       rm -rf ${pydocs} || die
+
+       in_path=$(python_get_sitedir)/${PN}
+
+       for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+       sed \
+               -e 's|#from __future__|from __future__|g' \
+               -i ${i} || die
+       done
+
+       insinto ${in_path}
+
+       dodir ${in_path}/c
+
+       ebegin "Installing main files"
+               doins -r python || die "main files installation failed"
+       eend
+               dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
+       for i in ${pydocs}; do
+               dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
+       done
+
+       dosym /usr/share/ccpn/data ${in_path}/data
+       dosym /usr/share/ccpn/model ${in_path}/model
+
+       einfo "Adjusting permissions"
+
+       files="
+               cambridge/c/BayesPeakSeparator.so
+               ccp/c/StructUtil.so
+               ccp/c/StructStructure.so
+               ccp/c/StructBond.so
+               ccp/c/StructAtom.so
+               ccpnmr/c/DyAtomCoord.so
+               ccpnmr/c/DyDistConstraint.so
+               ccpnmr/c/DyDistForce.so
+               ccpnmr/c/AtomCoordList.so
+               ccpnmr/c/DyAtomCoordList.so
+               ccpnmr/c/ContourStyle.so
+               ccpnmr/c/ContourLevels.so
+               ccpnmr/c/SliceFile.so
+               ccpnmr/c/PeakCluster.so
+               ccpnmr/c/Dynamics.so
+               ccpnmr/c/Bacus.so
+               ccpnmr/c/Midge.so
+               ccpnmr/c/DyDistConstraintList.so
+               ccpnmr/c/WinPeakList.so
+               ccpnmr/c/PeakList.so
+               ccpnmr/c/DistConstraint.so
+               ccpnmr/c/CloudUtil.so
+               ccpnmr/c/DistForce.so
+               ccpnmr/c/DistConstraintList.so
+               ccpnmr/c/AtomCoord.so
+               ccpnmr/c/DyDynamics.so
+               ccpnmr/c/ContourFile.so
+               memops/c/ShapeFile.so
+               memops/c/BlockFile.so
+               memops/c/PdfHandler.so
+               memops/c/MemCache.so
+               memops/c/FitMethod.so
+               memops/c/PsHandler.so
+               memops/c/GlHandler.so
+               memops/c/StoreFile.so
+               memops/c/StoreHandler.so
+               memops/c/TkHandler.so"
+       for FILE in ${files}; do
+               fperms 755 ${in_path}/python/${FILE}
+       done
+}
+
+pkg_postinst() {
+       python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+       python_mod_cleanup ${PN}
+}

diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis
index c94ee6a3a5011e8e8976d6fdc8a3b03c36039d1f..30250f09195eba63234a6572555bd680ac7deadf 100644 (file)
--- a/sci-chemistry/ccpn/files/analysis
+++ b/sci-chemistry/ccpn/files/analysis
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6

diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle
index f6f092c2e2568ee8f02a988a9f2c3eb84178ea7d..fe2bccb1107ff87167921f59c1eb27841f054a74 100644 (file)
--- a/sci-chemistry/ccpn/files/dangle
+++ b/sci-chemistry/ccpn/files/dangle
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6

diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter
index 80f2f4767f697ae99dd8a94e22bfcaa5919a4d68..a5b7f90599160487cf3367678ee5f153aa171453 100644 (file)
--- a/sci-chemistry/ccpn/files/dataShifter
+++ b/sci-chemistry/ccpn/files/dataShifter
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6

diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter
index 86ceb9dd85712712dbf0f18b1c85d83946eb6261..7f3a70f725e84b448d73cf0ddcf514db2098a583 100644 (file)
--- a/sci-chemistry/ccpn/files/depositionFileImporter
+++ b/sci-chemistry/ccpn/files/depositionFileImporter
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/pdbe/deposition/dataFileImport/dataFileImportGui.py $@

diff --git a/sci-chemistry/ccpn/files/eci b/sci-chemistry/ccpn/files/eci
index 043e639e5522b495f5c0ba761b7a79946dc8e594..40472bc06e8d8716c0cba995065fa920eeb84c03 100644 (file)
--- a/sci-chemistry/ccpn/files/eci
+++ b/sci-chemistry/ccpn/files/eci
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/eci/EntryCompletionGui.py $*

diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr
index 1c3edb64d2439d0445a96115d7fdbe15c323611c..e29298038c1325a6dc57b5d83a1a20f9f438f670 100644 (file)
--- a/sci-chemistry/ccpn/files/extendNmr
+++ b/sci-chemistry/ccpn/files/extendNmr
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@

diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter
index c23c510b54baa266e039500df5c287e9eff571f6..b310e0d6a42628fcf312495565a8b7de9aa24bb1 100644 (file)
--- a/sci-chemistry/ccpn/files/formatConverter
+++ b/sci-chemistry/ccpn/files/formatConverter
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6

diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara
index 6ee3546d8f1d9ec5d0b785034e5d011f57e89669..48b47342c5015e6ac8a4e688642ad2fc2296c3e2 100644 (file)
--- a/sci-chemistry/ccpn/files/pipe2azara
+++ b/sci-chemistry/ccpn/files/pipe2azara
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6

diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara
index 68db2bf57695282836673d8b1542494eda784863..f2775ade051054c7aa601ba91d8eea5ec96bd973 100644 (file)
--- a/sci-chemistry/ccpn/files/xeasy2azara
+++ b/sci-chemistry/ccpn/files/xeasy2azara
@@ -5,4 +5,5 @@ export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
 export LD_LIBRARY_PATH=gentoolibdir
 export TCL_LIBRARY=gentootcl
 export TK_LIBRARY=gentootk
+export PSIPRED_DIR=gentoousr
 gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6