diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/vienna-rna/ChangeLog | 5 | ||||
| -rw-r--r-- | sci-biology/vienna-rna/Manifest | 14 | ||||
| -rw-r--r-- | sci-biology/vienna-rna/metadata.xml | 42 |
3 files changed, 40 insertions, 21 deletions
diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog index d68bf4a80d64..72816ef39a7c 100644 --- a/sci-biology/vienna-rna/ChangeLog +++ b/sci-biology/vienna-rna/ChangeLog @@ -1,6 +1,9 @@ # ChangeLog for sci-biology/vienna-rna # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.15 2008/05/01 13:13:57 markusle Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.16 2008/08/06 15:06:58 ulm Exp $ + + 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml: + Add USE flag description to metadata wrt GLEP 56. *vienna-rna-1.7.0 (01 May 2008) diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest index 265b1681a9f7..0551aa362ab6 100644 --- a/sci-biology/vienna-rna/Manifest +++ b/sci-biology/vienna-rna/Manifest @@ -1,3 +1,6 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX vienna-rna-1.6.5-c-fixes.patch 728 RMD160 5f427bb976200f58599b1878ca7273844b21aac0 SHA1 7089237c787d780d53b92c4c38ba73ec60b81218 SHA256 49955a6244eb3be73f8d2472f3a4f9b8d1f8f92ba11327961b901a2c1f1e24d8 DIST ViennaRNA-1.4.tar.gz 483047 RMD160 31ce5f6e3f1adbd0c8e4759c243764523828a258 SHA1 fde493bfeeb443cb427bbe58b0d4daa446771ccf SHA256 8021ebe40d4fdf609fc9ad9aa7525736f69146666b6222d78d1016c20707522f DIST ViennaRNA-1.6.1.tar.gz 1149127 RMD160 37e4719e7ca03ced354976fa83f38d5f96776531 SHA1 afb35731c39893b17a21653a96ba5b3e39340934 SHA256 8036b6a562ec898dab4144cb5f18b42ff7c4290875572d05e7059b1ca2d5ddfd @@ -7,5 +10,12 @@ EBUILD vienna-rna-1.4.ebuild 2411 RMD160 df875d116e09cb23ae6fbda5d59bf12202584aa EBUILD vienna-rna-1.6.1.ebuild 1587 RMD160 563cb491bc5c71347eaacd0d093924fbba79afa6 SHA1 5d30247bf97f0cc2197993673dc1d813f27b37e1 SHA256 04308a39ccf800a738a899ff93b1592532dab2886405b90b99815c5e9155bead EBUILD vienna-rna-1.6.5.ebuild 1744 RMD160 1b8d7dc72c02d815a21fc1398865c1d936afaf05 SHA1 e05f78a86fd59fcb13c3e57fe462b93bc6c39b16 SHA256 6e5b9eff1e28e5a0ec47886d743abd1b79909cd2331f87daee75f66dddd9925e EBUILD vienna-rna-1.7.0.ebuild 1795 RMD160 35771c487766583375c59d513bd3bac59e2aaaa6 SHA1 01da384c1830df80f232c4e361b96a28b77acc81 SHA256 4a2044beeb9070f2c415c491b94eadb74972db2987806e524da1c7927686c499 -MISC ChangeLog 2420 RMD160 d399fa5a92415b32d438a63f28407944e3074c6e SHA1 094972a27d5cea1f0eeafea13601c3711ab0ea2a SHA256 8e59d9c4a8333026d36d74725ebc5d07e69a515d0f6b8ba99a31342211eed191 -MISC metadata.xml 1228 RMD160 8db8df2ec48d6a7e8dd4c592f7f4a9c7f8810cf9 SHA1 e46645ad44f1236a471a0ba79e08e4f6fe752dcb SHA256 7c558ba2568a5ec64654465c4c45784a32c4dccd6adf33518cf1f3daca2acd16 +MISC ChangeLog 2529 RMD160 de660b8d594fdcf6ba18ef4d29ad36f33e136a01 SHA1 5efc3d71998792750a265a7bb93320d9003ebbd7 SHA256 8b19d61deaa5672d40767abb837231c4373e39335281a4b37873fe114dbf1fd7 +MISC metadata.xml 1435 RMD160 539ba60c7a5ca6656e5716b61e2bbf44bb5b9c27 SHA1 77777cd6e84bb6e799e0bfb357580c6a3edfbb91 SHA256 93f911332c6232466324a14891ee9ede4fb23633b12b8ea42ed8cfa2c32b294b +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v1.4.9 (GNU/Linux) + +iEYEARECAAYFAkiZviQACgkQOeoy/oIi7uxE4gCgn48L64luVS6TcjyyPJadmaC4 +MaEAoIdUbY7PVKCIh+APR/1r9/sSvV2i +=9SS1 +-----END PGP SIGNATURE----- diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml index 5115aa6e1ee4..cec7b4a6ce48 100644 --- a/sci-biology/vienna-rna/metadata.xml +++ b/sci-biology/vienna-rna/metadata.xml @@ -1,22 +1,28 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <longdescription> - The Vienna RNA Package consists of a C code library and several - stand-alone programs for the prediction and comparison of RNA secondary - structures. RNA secondary structure prediction through energy - minimization is the most used function in the package. We provide three - kinds of dynamic programming algorithms for structure prediction: the - minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a - single optimal structure, the partition function algorithm of - (McCaskill 1990) which calculates base pair probabilities in the - thermodynamic ensemble, and the suboptimal folding algorithm of - (Wuchty et.al 1999) which generates all suboptimal structures within a - given energy range of the optimal energy. For secondary structure - comparison, the package contains several measures of distance - (dissimilarities) using either string alignment or tree-editing - (Shapiro and Zhang 1990). Finally, we provide an algorithm to design - sequences with a predefined structure (inverse folding). - </longdescription> +<herd>sci-biology</herd> +<longdescription> + The Vienna RNA Package consists of a C code library and several + stand-alone programs for the prediction and comparison of RNA secondary + structures. RNA secondary structure prediction through energy + minimization is the most used function in the package. We provide three + kinds of dynamic programming algorithms for structure prediction: the + minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a + single optimal structure, the partition function algorithm of + (McCaskill 1990) which calculates base pair probabilities in the + thermodynamic ensemble, and the suboptimal folding algorithm of + (Wuchty et.al 1999) which generates all suboptimal structures within a + given energy range of the optimal energy. For secondary structure + comparison, the package contains several measures of distance + (dissimilarities) using either string alignment or tree-editing + (Shapiro and Zhang 1990). Finally, we provide an algorithm to design + sequences with a predefined structure (inverse folding). +</longdescription> +<use> + <flag name='no-readseq'>Do not include the modified version of Don Gilbert's + readseq program</flag> + <flag name='no-utils'>Do not include sequence format conversion and + representation utilities</flag> +</use> </pkgmetadata> |