diff options
| -rw-r--r-- | sci-biology/bioperl-run/Manifest | 16 | ||||
| -rw-r--r-- | sci-biology/bioperl/ChangeLog | 9 | ||||
| -rw-r--r-- | sci-biology/bioperl/Manifest | 26 | ||||
| -rw-r--r-- | sci-biology/bioperl/bioperl-1.5.1.ebuild | 52 | ||||
| -rw-r--r-- | sci-biology/bioperl/files/digest-bioperl-1.5.1 | 3 |
5 files changed, 87 insertions, 19 deletions
diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest index 5a918ac3d2d0..8855d8369e11 100644 --- a/sci-biology/bioperl-run/Manifest +++ b/sci-biology/bioperl-run/Manifest @@ -3,14 +3,19 @@ MD5 21ad123058f1e670f289ee1a87de4e82 files/bioperl-run-Pise-test-patch.diff 722 RMD160 85c3744bfc14db91971e4df2dfd967c5ad9f0310 files/bioperl-run-Pise-test-patch.diff 722 SHA256 84c8280f8d3af311b53c8b6edd4e6ffa9acc0824528d96d7f1c2537404d3e30f files/bioperl-run-Pise-test-patch.diff 722 DIST bioperl-run-1.4.tar.gz 830774 +DIST bioperl-run-1.5.1.tar.gz 864369 RMD160 841e33cffda7b787b1700a075bf985c717d7e678 SHA1 35d4ab009f7e653dd18bb636854181d68841b613 SHA256 d9e1f5bdff5541376cab1c8b7e8db9bedbbb7b6f76b965d55dc20122a98f93e8 EBUILD bioperl-run-1.4.ebuild 1303 RMD160 042856b0ab449d9ffe203d4c0515f96c75b9930c SHA1 7dce164a3042784cf7ebdffdac3fa8a7447e318e SHA256 8d9a807e7e4cf4deff1b0f7cdc405bc324410c882bc70915128b70656b1a0ab2 MD5 ede6a317da6b1ba511beeb256cb71453 bioperl-run-1.4.ebuild 1303 RMD160 042856b0ab449d9ffe203d4c0515f96c75b9930c bioperl-run-1.4.ebuild 1303 SHA256 8d9a807e7e4cf4deff1b0f7cdc405bc324410c882bc70915128b70656b1a0ab2 bioperl-run-1.4.ebuild 1303 -MISC ChangeLog 2069 RMD160 147bfc11b0fa887418b30095dd0473168f1ce1ea SHA1 a3a156d20bceb901bfa206f15ecc0e026c2bdf6e SHA256 7b8f7dd2d184dd4b5d34ac02cb0cffd6e3e24153ae5f06e8fd7b3237bcb56bfa -MD5 3aa2552cccf16c1d5ed8257a66c1817d ChangeLog 2069 -RMD160 147bfc11b0fa887418b30095dd0473168f1ce1ea ChangeLog 2069 -SHA256 7b8f7dd2d184dd4b5d34ac02cb0cffd6e3e24153ae5f06e8fd7b3237bcb56bfa ChangeLog 2069 +EBUILD bioperl-run-1.5.1.ebuild 1317 RMD160 88759d2c332ab697df218a6891a955e802e4c7fb SHA1 3fe1fb83b28519b84cd6974799010290ae0a1767 SHA256 5b9f96241cb4c596cd29f09e76341689f6894180524f71f601c39bf7608b87b0 +MD5 93851d113efb98707cab36dea4a7ac21 bioperl-run-1.5.1.ebuild 1317 +RMD160 88759d2c332ab697df218a6891a955e802e4c7fb bioperl-run-1.5.1.ebuild 1317 +SHA256 5b9f96241cb4c596cd29f09e76341689f6894180524f71f601c39bf7608b87b0 bioperl-run-1.5.1.ebuild 1317 +MISC ChangeLog 2227 RMD160 d690061c79df87ef0fb4841834f08e3737542106 SHA1 580569ec7582b9194c2d408dbd5f7a188bb9bae6 SHA256 035174f0ad5779626502c93894c768b02723d292d76c88391dc493692aaff3d8 +MD5 b7b77346f0546be54077e1469ad28088 ChangeLog 2227 +RMD160 d690061c79df87ef0fb4841834f08e3737542106 ChangeLog 2227 +SHA256 035174f0ad5779626502c93894c768b02723d292d76c88391dc493692aaff3d8 ChangeLog 2227 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262 @@ -18,3 +23,6 @@ SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f metadata MD5 47db6a1f839dd45f8c891b5f6ab2ff2a files/digest-bioperl-run-1.4 67 RMD160 ea531db028c33bfb9ddd97545bfb5f852010f6d2 files/digest-bioperl-run-1.4 67 SHA256 aa030e3823bd4e0cf56adc1264604e473fec0720814b358dd08472a7c28efe0a files/digest-bioperl-run-1.4 67 +MD5 388741fe73c4ca46a581b02689f13a74 files/digest-bioperl-run-1.5.1 253 +RMD160 864b8a2e16d7c2032c71dd099c266e6ff049def3 files/digest-bioperl-run-1.5.1 253 +SHA256 1cead595c5b1249d6ea254820bfeeca26ca2fbab4c094304cc28f8b3f4f4b7b2 files/digest-bioperl-run-1.5.1 253 diff --git a/sci-biology/bioperl/ChangeLog b/sci-biology/bioperl/ChangeLog index 9c759516f987..cf54b1ed0d7d 100644 --- a/sci-biology/bioperl/ChangeLog +++ b/sci-biology/bioperl/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/bioperl # Copyright 2002-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.21 2006/08/18 02:21:58 mcummings Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.22 2006/09/13 01:41:58 ribosome Exp $ + +*bioperl-1.5.1 (13 Sep 2006) + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +bioperl-1.5.1.ebuild: + New upstream version. Thanks to Greg Wilson <gdw1@cornell.edu>, Martin + Mokrejs <mmokrejs@ribosome.natur.cuni.cz> and Neil Shephard + <nshephard@gmail.com> for their work (see bug #79459). 18 Aug 2006; Michael Cummings <mcummings@gentoo.org> bioperl-1.4.ebuild: Marking amd64 stable diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest index 66f22fb21581..9ff9f131262f 100644 --- a/sci-biology/bioperl/Manifest +++ b/sci-biology/bioperl/Manifest @@ -1,15 +1,17 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST bioperl-1.4.tar.bz2 4224508 RMD160 657170cc17655f2ab9ed5f6509cac5ae7eedd2c3 SHA1 d0683ff46ef304c04a40296561065d78baa0d787 SHA256 5ba68ce688ac4f079057e03b5bfca60f410d9eb68961d03b62ae75050718687b +DIST bioperl-1.5.1.tar.bz2 5538613 RMD160 422bdd0dc17dd246ec1fc3ae6fe020705111892d SHA1 9841a458fd928eb9715f14eb686c7b1af3a379e7 SHA256 696c8bd162bc79fa3c75eeb63bb42f8cbcbb4b72de4dcb3bec7ea7a293506f6c EBUILD bioperl-1.4.ebuild 1175 RMD160 3a873722d4d53220920e4602c6bfa618ae3b9e79 SHA1 82e785042540409b671959a63b9c3a9232495d94 SHA256 dc8b5b849884b106630deedd2e5fe759f9b304e87b71ff3cb4c6b30a4a1dd560 MD5 de99ea907d1aaae79d2ed082d3c5ffcc bioperl-1.4.ebuild 1175 RMD160 3a873722d4d53220920e4602c6bfa618ae3b9e79 bioperl-1.4.ebuild 1175 SHA256 dc8b5b849884b106630deedd2e5fe759f9b304e87b71ff3cb4c6b30a4a1dd560 bioperl-1.4.ebuild 1175 -MISC ChangeLog 4939 RMD160 4650b7d341fdafacc7ad8bc057d2e67f53c4bcb1 SHA1 fe943fda3b740c4d3c3c286c189780a54a191289 SHA256 1c8480b9819a443798e26b993b6d8c200caed33a01ddd902a8c31108c7e48e2d -MD5 0b394facb896b9bd9589007965ef3100 ChangeLog 4939 -RMD160 4650b7d341fdafacc7ad8bc057d2e67f53c4bcb1 ChangeLog 4939 -SHA256 1c8480b9819a443798e26b993b6d8c200caed33a01ddd902a8c31108c7e48e2d ChangeLog 4939 +EBUILD bioperl-1.5.1.ebuild 1197 RMD160 b3a92d8eba1f2d3da639ee4a33b469619f40a0ef SHA1 d87b74cef60fdb9a8991d76efc9b8ac54c49b0a8 SHA256 2c8915c6ddc0726b277994a605ccf96082665f3968b4bb6a04348c700b7a82df +MD5 fa4383b2076e0db29a7c0babebc2129b bioperl-1.5.1.ebuild 1197 +RMD160 b3a92d8eba1f2d3da639ee4a33b469619f40a0ef bioperl-1.5.1.ebuild 1197 +SHA256 2c8915c6ddc0726b277994a605ccf96082665f3968b4bb6a04348c700b7a82df bioperl-1.5.1.ebuild 1197 +MISC ChangeLog 5237 RMD160 45f121a54f97e27b229df8c9acb2314ced9874c9 SHA1 0f06a705640957bb273f893f08f2ebcd75b27db6 SHA256 9682b5d4b99260334ce52045726b41dc126d60c11c9156fb07b8633405c83281 +MD5 c4ecfac840042e32f78102e10d932291 ChangeLog 5237 +RMD160 45f121a54f97e27b229df8c9acb2314ced9874c9 ChangeLog 5237 +SHA256 9682b5d4b99260334ce52045726b41dc126d60c11c9156fb07b8633405c83281 ChangeLog 5237 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262 @@ -17,10 +19,6 @@ SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f metadata MD5 4615cdeb82040a54abfe906737fbbe80 files/digest-bioperl-1.4 241 RMD160 be4f220380af8e6d9050fb970f4afa9007cc5322 files/digest-bioperl-1.4 241 SHA256 7f2cfe5a68d98c143ebc904b1c54de78d21218c225a93870256ea74c3d043fd1 files/digest-bioperl-1.4 241 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v1.4.4 (GNU/Linux) - -iD8DBQFE5SRMtG5z4I8BtQoRAknVAJ92Zxq8vCg/QkldP76xVbLbJwEnMwCfYidy -QuBy3b+onXSYCsQQ+KN8brs= -=IaNG ------END PGP SIGNATURE----- +MD5 970b42591ef0cc641b037271250cb250 files/digest-bioperl-1.5.1 247 +RMD160 772c74652407b0ed6de23eb6b5c4a524134dacd2 files/digest-bioperl-1.5.1 247 +SHA256 92906734ae731b92c7acee45ed4a0e7827a47f6e4dc4a214e6049ac95734f1d3 files/digest-bioperl-1.5.1 247 diff --git a/sci-biology/bioperl/bioperl-1.5.1.ebuild b/sci-biology/bioperl/bioperl-1.5.1.ebuild new file mode 100644 index 000000000000..1053a8daeeeb --- /dev/null +++ b/sci-biology/bioperl/bioperl-1.5.1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.5.1.ebuild,v 1.1 2006/09/13 01:41:58 ribosome Exp $ + +inherit perl-module eutils + +CATEGORY="sci-biology" + +DESCRIPTION="collection of tools for bioinformatics, genomics and life science research" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="http://www.bioperl.org/DIST/${P}.tar.bz2" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~sparc ~x86" +IUSE="mysql gd" + +DEPEND=" + perl-core/File-Temp + dev-perl/HTML-Parser + dev-perl/IO-String + dev-perl/IO-stringy + dev-perl/SOAP-Lite + perl-core/Storable + dev-perl/XML-DOM + dev-perl/XML-Parser + dev-perl/XML-Writer + dev-perl/XML-Twig + dev-perl/libxml-perl + dev-perl/libwww-perl + dev-perl/Graph + dev-perl/Text-Shellwords + gd? ( + >=dev-perl/GD-1.32-r1 + dev-perl/SVG + dev-perl/GD-SVG + ) + mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )" + +src_compile() { + yes "" | perl Makefile.PL ${myconf} \ + PREFIX=${D}/usr INSTALLDIRS=vendor +} + +src_test() { + perl-module_src_test || die "Test failed" +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/files/digest-bioperl-1.5.1 b/sci-biology/bioperl/files/digest-bioperl-1.5.1 new file mode 100644 index 000000000000..299158ff7ff2 --- /dev/null +++ b/sci-biology/bioperl/files/digest-bioperl-1.5.1 @@ -0,0 +1,3 @@ +MD5 ba24f59a00c9919840a9b58f7fbd4d94 bioperl-1.5.1.tar.bz2 5538613 +RMD160 422bdd0dc17dd246ec1fc3ae6fe020705111892d bioperl-1.5.1.tar.bz2 5538613 +SHA256 696c8bd162bc79fa3c75eeb63bb42f8cbcbb4b72de4dcb3bec7ea7a293506f6c bioperl-1.5.1.tar.bz2 5538613 |