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author | 2011-05-03 11:10:40 +0000 | |
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committer | 2011-05-03 11:10:40 +0000 | |
commit | e427b21940169f8d4f11465d12a3f4bb992b9239 (patch) | |
tree | d8424b8abe6e3a180a6ea9c65c7a5242dba6a36d /sci-biology | |
parent | x86 stable wrt security bug #365751 (diff) | |
download | historical-e427b21940169f8d4f11465d12a3f4bb992b9239.tar.gz historical-e427b21940169f8d4f11465d12a3f4bb992b9239.tar.bz2 historical-e427b21940169f8d4f11465d12a3f4bb992b9239.zip |
Added python support, #365793
Package-Manager: portage-2.2.0_alpha30/cvs/Linux x86_64
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/vienna-rna/ChangeLog | 6 | ||||
-rw-r--r-- | sci-biology/vienna-rna/Manifest | 11 | ||||
-rw-r--r-- | sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py | 27 | ||||
-rw-r--r-- | sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild | 21 |
4 files changed, 55 insertions, 10 deletions
diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog index a8f3e2425b32..1e04ac61d6d4 100644 --- a/sci-biology/vienna-rna/ChangeLog +++ b/sci-biology/vienna-rna/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/vienna-rna # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.36 2011/03/20 20:32:09 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.37 2011/05/03 11:10:40 jlec Exp $ + + 03 May 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.5.ebuild, + +files/vienna-rna-1.8.5-setup.py: + Added python support, #365793 20 Mar 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.4-r1.ebuild, vienna-rna-1.8.4-r2.ebuild, vienna-rna-1.8.5.ebuild: diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest index 8e176ce94951..4970a9a22d89 100644 --- a/sci-biology/vienna-rna/Manifest +++ b/sci-biology/vienna-rna/Manifest @@ -9,17 +9,18 @@ AUX vienna-rna-1.8.4-bindir.patch 351 RMD160 e12b774a2c8224ed85785f9e3994a48b3d8 AUX vienna-rna-1.8.4-implicits.patch 1163 RMD160 489b9a557c7cae23da0491ba7f5f8728a3832f10 SHA1 4cb39153f57bec07d38aead97fc20cd29828e54e SHA256 f49e60dc866e7844fea32e90b9e91ceb0b06cf937f52781179938519e618cf1a AUX vienna-rna-1.8.4-jobserver-fix.patch 681 RMD160 c72649a57ece3d511cc18f2cac47c7ab103c258d SHA1 0c5e67318c826f12553cf8cb807c3061c1e70574 SHA256 bec5248214ba303d85afda03e663f84061258cd06f2f50773011251299a42b84 AUX vienna-rna-1.8.4-overflows.patch 740 RMD160 ec5f8a0f22eb7ddc845d515cd7896e90d31ecdbd SHA1 084eea746bf2ae44775063397baa2f9314a05bde SHA256 cd977c5acfca05890768893ab5e18fca5fee167dac341e0edd16bc4fd7cd2a08 +AUX vienna-rna-1.8.5-setup.py 810 RMD160 17d3ab6751ac139b73a502ad9057ffdaea1534db SHA1 c936bff8e20c1125421849cf4640fee13be59e35 SHA256 91e4caa304aa97430552f2a3a46f57ced23239d55b1a52a658bbcf91e0835f62 DIST ViennaRNA-1.8.4.tar.gz 1397733 RMD160 29939511e560d898164c21d2452316b0a3a6771e SHA1 6e3a0751849f1b43d4751ce64670a21a3718f040 SHA256 90a5408d05f7dd35031a527d1823607daa8fc8f394b438fb072be78afc7174b7 DIST ViennaRNA-1.8.5.tar.gz 1306792 RMD160 5c67030f4e9ff2f5d8c4595178c030781f3a2e56 SHA1 c20dd5ffa6d46ea48de5dd1f3d5e6eff8ae2d385 SHA256 f4e2d94beaf77165e8321758e4ab0ad1c5d49879cefa12e48b07d09ed2d0ecf9 EBUILD vienna-rna-1.8.4-r1.ebuild 2468 RMD160 6387fa11fa9278b537a6837a698b3b5d9499e079 SHA1 4c0381decae077e485a69ad4e44ddc013dd66174 SHA256 ee60fe00e65ade7cce7fe7b039fe3d2ad3ab960dcff2cd5ada4388804a17e73e EBUILD vienna-rna-1.8.4-r2.ebuild 2338 RMD160 d190f65fccb687f499f10f9e3b6b64626933f645 SHA1 fa5a38377f1481748fb83acf2be9658de9a99cee SHA256 e762b0a04f2288f0c767f888d874c8ef0abcb722999f619398be2b2516fd1959 -EBUILD vienna-rna-1.8.5.ebuild 2295 RMD160 269bc0056204bb79b1abe8d63b7cf8d9e780cc2e SHA1 f1d966fa374a34ac9ecab0d5fd43944143b3a90c SHA256 4410f366daac744049d0edf295a49c99d05af3aaf57afa34bf09131e23a92f9f -MISC ChangeLog 5849 RMD160 af5ed4a66ed9ef4673f5533c2c0f1b911765fd06 SHA1 58d4f37bc6264e89a52b80ffa28036d7f2536b1a SHA256 9f1fa27cf4b2929d971920687ae9398ae8f931156b9e1026cb7796a1d3221fcf +EBUILD vienna-rna-1.8.5.ebuild 2630 RMD160 7290cea1b92bc51c57316c3941a182873070725a SHA1 e0ae283459591cc61145e2d5962d4d1350f748de SHA256 36d0cdabe333f6140dafa2bc10cb2e5a6b14a2009b7f4aef4de86fa5c09cce41 +MISC ChangeLog 5990 RMD160 b3e653ef4eb7a70aa2c035fcece729f1c28af968 SHA1 65e228449f07aae3532ec627d3f2361c9c61a445 SHA256 969311c92585a43eca8a8d68d053ff8f7bbbb78e7118e46fcfa74d3f2c3ff3fd MISC metadata.xml 1210 RMD160 41d50f7af8428b196c4ef855b68dcb657588bb34 SHA1 08f8e1aa88086fd9a3f5fa03fa46c31e12a3f776 SHA256 9c8b3f60f6098accff7c67f26ea07cb5b57e9ed8eae5d3d03949f1718ab6517e -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk2GZE8ACgkQgAnW8HDreRY1CgCfXjseoh3Io5WpvP/Olqw/utSl -uC4AniHz9QvDC+t9x4Q5pGZf9/aOoHSD -=tnL7 +iEYEARECAAYFAk2/4rUACgkQgAnW8HDreRZTpACghcTcjtyPQm4RhG5W2/Pd0c0B +StkAnjB7q3NRYofEON1E/0HMvlnpc1fF +=USCD -----END PGP SIGNATURE----- diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py new file mode 100644 index 000000000000..0aeaf2a116d3 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py @@ -0,0 +1,27 @@ +from distutils.core import setup, Extension +import os +import sys + +old_filename = os.path.join("Perl", "RNA.py") +new_filename = os.path.join("Perl", "__init__.py") +if os.path.exists(old_filename): + os.rename(old_filename, new_filename) + +extra_link_args = [] + +extension = Extension("_RNA", + ["Perl/RNA_wrap.c"], + libraries=['RNA'], + library_dirs=['lib'], + extra_link_args=extra_link_args + ) + +setup(name="RNA", + version="1.8.5", + description="Vienna RNA", + author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", + url="http://www.tbi.univie.ac.at/RNA/", + package_dir = {'RNA':'Perl'}, + packages = ['RNA'], + ext_modules=[extension], + ) diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild index b3264d75e9d4..c35237931503 100644 --- a/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild +++ b/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild @@ -1,10 +1,13 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild,v 1.2 2011/03/20 20:32:09 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild,v 1.3 2011/05/03 11:10:40 jlec Exp $ -EAPI="2" +EAPI="3" -inherit toolchain-funcs multilib autotools perl-module +PYTHON_DEPEND="python? 2" +SUPPORT_PYTHON_ABIS="1" + +inherit distutils toolchain-funcs multilib autotools perl-module DESCRIPTION="RNA secondary structure prediction and comparison" HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" @@ -12,7 +15,7 @@ SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz" LICENSE="vienna-rna" SLOT="0" -IUSE="" +IUSE="python" KEYWORDS="~amd64 ~ppc ~x86" DEPEND=" @@ -40,6 +43,7 @@ src_prepare() { eautoreconf cd RNAforester && eautoreconf + use python && cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py } src_configure() { @@ -57,6 +61,14 @@ src_compile() { emake || die emake -C Readseq || die "Failed to compile readseq." # TODO: Add (optional?) support for the NCBI toolkit. + if use python; then + pushd Perl > /dev/null + mv RNA_wrap.c{,-perl} + swig -python RNA.i + popd > /dev/null + distutils_src_compile + mv Perl/RNA_wrap.c{-perl,} + fi } src_test() { @@ -74,4 +86,5 @@ src_install() { # remove perlocal.pod to avoid file collisions (see #240358) fixlocalpod || die "Failed to remove perlocal.pod" + use python && distutils_src_install } |