From 84ab789f69edbf17446b640ecb485accbabcc3e4 Mon Sep 17 00:00:00 2001 From: Sergei Trofimovich Date: Tue, 10 Mar 2015 21:58:42 +0000 Subject: [PATCH] =?utf8?q?A=20bioinformatics=20library=20for=20haskell=20(?= =?utf8?q?requested=20by=20Martin=20MOKREJ=C5=A0).?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit Package-Manager: portage-2.2.17/cvs/Linux x86_64 Manifest-Sign-Key: 0x611FF3AA --- dev-haskell/biocore/ChangeLog | 9 ++++++ dev-haskell/biocore/Manifest | 14 +++++++++ dev-haskell/biocore/biocore-0.3.1.ebuild | 26 ++++++++++++++++ dev-haskell/biocore/metadata.xml | 11 +++++++ dev-haskell/biofasta/ChangeLog | 9 ++++++ dev-haskell/biofasta/Manifest | 14 +++++++++ dev-haskell/biofasta/biofasta-0.0.3.ebuild | 26 ++++++++++++++++ dev-haskell/biofasta/metadata.xml | 8 +++++ dev-haskell/biosff/ChangeLog | 9 ++++++ dev-haskell/biosff/Manifest | 14 +++++++++ dev-haskell/biosff/biosff-0.3.7.1.ebuild | 36 ++++++++++++++++++++++ dev-haskell/biosff/metadata.xml | 15 +++++++++ 12 files changed, 191 insertions(+) create mode 100644 dev-haskell/biocore/ChangeLog create mode 100644 dev-haskell/biocore/Manifest create mode 100644 dev-haskell/biocore/biocore-0.3.1.ebuild create mode 100644 dev-haskell/biocore/metadata.xml create mode 100644 dev-haskell/biofasta/ChangeLog create mode 100644 dev-haskell/biofasta/Manifest create mode 100644 dev-haskell/biofasta/biofasta-0.0.3.ebuild create mode 100644 dev-haskell/biofasta/metadata.xml create mode 100644 dev-haskell/biosff/ChangeLog create mode 100644 dev-haskell/biosff/Manifest create mode 100644 dev-haskell/biosff/biosff-0.3.7.1.ebuild create mode 100644 dev-haskell/biosff/metadata.xml diff --git a/dev-haskell/biocore/ChangeLog b/dev-haskell/biocore/ChangeLog new file mode 100644 index 000000000000..413e1bc80fed --- /dev/null +++ b/dev-haskell/biocore/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-haskell/biocore +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/dev-haskell/biocore/ChangeLog,v 1.1 2015/03/10 21:57:29 slyfox Exp $ + +*biocore-0.3.1 (10 Mar 2015) + + 10 Mar 2015; Sergei Trofimovich +biocore-0.3.1.ebuild, + +metadata.xml: + A bioinformatics library for haskell (requested by Martin MOKREJÅ ). diff --git a/dev-haskell/biocore/Manifest b/dev-haskell/biocore/Manifest new file mode 100644 index 000000000000..4cb40db7fae2 --- /dev/null +++ b/dev-haskell/biocore/Manifest @@ -0,0 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST biocore-0.3.1.tar.gz 2812 SHA256 212b7d7395138d4c231968e1f5bb047c03f61adc6c5eb36162602f42c24db41a SHA512 0a9a3690aa0888c688c8429facd0a26ac94f639222568d2e68a0640714098a40fa38d196800900486d12b36ee735576519d98e4d45f0320261d3f5de9ab09311 WHIRLPOOL 5aa7efb0e687127c947b489599b14096e1e50d7e58c70c3e0e98807d6b8085d13e1515da3f511da9d366a6af8abbeba439bf348974edffecb12953207f7d9228 +EBUILD biocore-0.3.1.ebuild 699 SHA256 59754497164474913769cf5fba28916a6db3d761ee09d53e80e08a677b8a9ef6 SHA512 e84189e048e4ae767f228e9de1a65619e22db743e689d9ccbd6fef7b3f48d26be4b99b13cae78ab1685591bb70b4cb7f1b9b8932e03f1953a551fe52ee359442 WHIRLPOOL 8ef278fb086b472f1baa1eb4e6ad9d2749376d4a481adcdc807af42783a48434d4938667613206ac1b961c15ffa1221e26c47fdcb11187a8f0c507acfae2b3a9 +MISC ChangeLog 406 SHA256 181d66292f8dd5c76e96101d08fe6cfd5cc6a683a8994c9c7feb9b69b5bff90d SHA512 89ff5add4a005e7ccdfc77985a28502348a9fe148a7017d3657c8c90088feca059e1497d8c9cdcc9ef2e4673f7553e045aaefa2f475dd75521eecce88aa24d02 WHIRLPOOL 429ae7f52bde19b8b0b520f55afc16f32de56ed8a6d22f906e126b27c489fefefb57798c46763636fba6c037384c9ed2eb228149c9864a426330a1e6e85e0899 +MISC metadata.xml 425 SHA256 2473a1a5f5f1e232be01453b27f2eeeead3a740d463b3090af5e5c003778be51 SHA512 e9b4311b197373d385dd20fb17c2f3bdf7a48ec2eb5476f82dff3fad654cf291cc64ccaca876a8e2337f95358e9e09c3cf795cc2dbf6d517e343f68208c93009 WHIRLPOOL a1c92eb280b5ccde68730bcd55ed178c323bb2d61f90cbaf5e4c2ab8ec8a655aa0c25d9ad8d8637cd20acd12dff1b682374a6727891ab9da851fede72ef918ad +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2 + +iEYEAREIAAYFAlT/aLQACgkQcaHudmEf86rwqgCfWddouWYmwTs3/9X9rorrmG74 +ez4AnRs1fRE9Z2mkCjzI0LwzKe01GJKk +=gU2p +-----END PGP SIGNATURE----- diff --git a/dev-haskell/biocore/biocore-0.3.1.ebuild b/dev-haskell/biocore/biocore-0.3.1.ebuild new file mode 100644 index 000000000000..17684dffb8d8 --- /dev/null +++ b/dev-haskell/biocore/biocore-0.3.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/dev-haskell/biocore/biocore-0.3.1.ebuild,v 1.1 2015/03/10 21:57:29 slyfox Exp $ + +EAPI=5 + +# ebuild generated by hackport 0.3.3.9999 + +CABAL_FEATURES="lib profile haddock hoogle hscolour" +inherit haskell-cabal + +DESCRIPTION="A bioinformatics library" +HOMEPAGE="http://hackage.haskell.org/package/biocore" +SRC_URI="mirror://hackage/packages/archive/${PN}/${PV}/${P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="dev-haskell/stringable:=[profile?] + >=dev-lang/ghc-6.10.4:= +" +DEPEND="${RDEPEND} + >=dev-haskell/cabal-1.6.0.3 +" diff --git a/dev-haskell/biocore/metadata.xml b/dev-haskell/biocore/metadata.xml new file mode 100644 index 000000000000..738abba90547 --- /dev/null +++ b/dev-haskell/biocore/metadata.xml @@ -0,0 +1,11 @@ + + + + haskell + + A set of core definitions and data structures + commonly used in bioinformatics. The intention is that bioinformatics + libraries will use this as a common ground to avoid needless incompatibilities + and duplicated work. + + diff --git a/dev-haskell/biofasta/ChangeLog b/dev-haskell/biofasta/ChangeLog new file mode 100644 index 000000000000..efb7bcdccfc7 --- /dev/null +++ b/dev-haskell/biofasta/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-haskell/biofasta +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/dev-haskell/biofasta/ChangeLog,v 1.1 2015/03/10 21:58:18 slyfox Exp $ + +*biofasta-0.0.3 (10 Mar 2015) + + 10 Mar 2015; Sergei Trofimovich +biofasta-0.0.3.ebuild, + +metadata.xml: + A bioinformatics library for haskell (requested by Martin MOKREJÅ ). diff --git a/dev-haskell/biofasta/Manifest b/dev-haskell/biofasta/Manifest new file mode 100644 index 000000000000..27a76dec0159 --- /dev/null +++ b/dev-haskell/biofasta/Manifest @@ -0,0 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST biofasta-0.0.3.tar.gz 14468 SHA256 6221a89cde259e8f9a2d4da11230a8a53d78b24d3367e70be5e7b1279e06e7d0 SHA512 de50d2f499fc0ee532b5ca28dff868c3dd0d243eaadeb1a4e3a3ebb913812f3308f581aefbf79806d58535b1f78ae283660b5a2348da1a9535f4d48f96b8678e WHIRLPOOL ae31bd9beaa62d3e1994dcc447fdf6c88fc8148b141be4b41cd4d3fec144d306905ece35313bbf165fddf0e4e0c66dae0250f85ebafadcefbe817f194d80dbec +EBUILD biofasta-0.0.3.ebuild 723 SHA256 51ba7534d73d605b281bf2a1121706ed355332f36ac6c893d2f231f0721bea74 SHA512 bb5e92d931cdd08fbe98f72177286b7fdadf4f566ebc3e340c0e2819e0eafd3c8832c474f5ac3e7ac7233689d2e8a6a863ceff81f7a61912912d6f901797f6a2 WHIRLPOOL 429781592c715ebae588fb1e4e5c0a7d41f5e6ebb781ce1de6e380da1803f8bec3a40d5cb78ee1f747b92d630f2528b0cf50bbfdc7b4750629ce3ba094a1ce45 +MISC ChangeLog 410 SHA256 4165870b75e6ad63b73952560e8efa0c71313a8462ad7d672b784f8acabbee90 SHA512 5ef7107f48367a7c98d3e5cb17595ffe730f799ba46f972cc508ba0ce72bd7db3fcd19b70847c8d7f17aee617a3bc511b743cdb20e6dde5ba1513722c42bcb9d WHIRLPOOL 6005845d599c0259c35ca0d00c9198d4cc5559fba0f45bee55eb829a3d9750d3b69c2391f645e8d0dd3ef767bbd29bae35acf713a172b891b9ca6e6046739399 +MISC metadata.xml 243 SHA256 959484015573861f3ef4b88128c526544ee16c7b8e97904ec3e88a290ac5753a SHA512 cc43052afa49f274ae2891d327c5bf2b5f1e09aab39239ef5c650320fbbafc8b00e3037ec4cbf10f2640d2350704b6efcc8c8b73a784ca5ca6edf6d411ab384e WHIRLPOOL 0967d29c4c4b3f5c309b50e0e779da9de25766e4d48808e4f31f2e0c11c27f3cde498768df44c22737652a20d391f0453fc5a69b0e1b3bbb5831cf16dd28c4c7 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2 + +iEYEAREIAAYFAlT/aOUACgkQcaHudmEf86q8WgCdFnDOPvBaDr7y1kiHqyp48ZPm +FQQAn18Z2MrykTKnVUROCQcUYCnV0nHh +=Vr+J +-----END PGP SIGNATURE----- diff --git a/dev-haskell/biofasta/biofasta-0.0.3.ebuild b/dev-haskell/biofasta/biofasta-0.0.3.ebuild new file mode 100644 index 000000000000..06abeb7c7e9c --- /dev/null +++ b/dev-haskell/biofasta/biofasta-0.0.3.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/dev-haskell/biofasta/biofasta-0.0.3.ebuild,v 1.1 2015/03/10 21:58:18 slyfox Exp $ + +EAPI=5 + +# ebuild generated by hackport 0.3.3.9999 + +CABAL_FEATURES="lib profile haddock hoogle hscolour" +inherit haskell-cabal + +DESCRIPTION="Library for reading fasta sequence files" +HOMEPAGE="https://patch-tag.com/r/dfornika/biofasta/home" +SRC_URI="mirror://hackage/packages/archive/${PN}/${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=">=dev-haskell/biocore-0.3.1:=[profile?] + >=dev-lang/ghc-6.10.4:= +" +DEPEND="${RDEPEND} + >=dev-haskell/cabal-1.6.0.3 +" diff --git a/dev-haskell/biofasta/metadata.xml b/dev-haskell/biofasta/metadata.xml new file mode 100644 index 000000000000..e2d400a97c00 --- /dev/null +++ b/dev-haskell/biofasta/metadata.xml @@ -0,0 +1,8 @@ + + + + haskell + + Library for reading fasta sequence files + + diff --git a/dev-haskell/biosff/ChangeLog b/dev-haskell/biosff/ChangeLog new file mode 100644 index 000000000000..7fa79a697550 --- /dev/null +++ b/dev-haskell/biosff/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-haskell/biosff +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/dev-haskell/biosff/ChangeLog,v 1.1 2015/03/10 21:58:41 slyfox Exp $ + +*biosff-0.3.7.1 (10 Mar 2015) + + 10 Mar 2015; Sergei Trofimovich +biosff-0.3.7.1.ebuild, + +metadata.xml: + A bioinformatics library for haskell (requested by Martin MOKREJÅ ). diff --git a/dev-haskell/biosff/Manifest b/dev-haskell/biosff/Manifest new file mode 100644 index 000000000000..9f28a9f8f839 --- /dev/null +++ b/dev-haskell/biosff/Manifest @@ -0,0 +1,14 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST biosff-0.3.7.1.tar.gz 26705 SHA256 982f238e056c3d65bae94c505da61e91239b624a8446ecee3b03eae258c7bad7 SHA512 ce075d734864b9a00999d5c37c824ece5ba475b583536eb842835b4a44ff56581f18ba8ddf065f2ea4416ff4f96279f6a46f5e57330a43d40164f4cabab2ab9f WHIRLPOOL 5bfb9b47df171165e9a4f03df7b3ec54c7dd07d784940409f703cb51b844449e46329164546525d9a49f8462d9bc0863d9c053b2d9d67d59e21cf99d0829d271 +EBUILD biosff-0.3.7.1.ebuild 977 SHA256 77695a66c2347eea9dc811f479eacd5bcb3e1835c717da0f7b496134181b3a8b SHA512 76e9acb0e9653d3518fea2fcc26b58c95570fe15f1cae9081dab4831711766216b088ee1e26ac81bde15633be0a7bbf2f9bf3aab3d6fea971d6ac428db1d4aff WHIRLPOOL d358db5f29ce6309ce29fb2d565d0bac1ea2e24040a7a9d559c95abb175f17a5ea25d386b6ec3a310380a263e9f894a79c629ce112adc01af2d4f1bc1ade0596 +MISC ChangeLog 406 SHA256 cf1e5eeda25c870d24f783f225648b09f75b8f1bae71ba6212f59897a14ee700 SHA512 0c322cc73d4e04a959897ef68cafda01b5b7046c815c1292dd23462ef5018ecebda3081c68c2c08fcc6d82a6c6a097aef2eac9c793bbcef92c13d09ef83ceb50 WHIRLPOOL d4823fca7377d841d00c85bd8faffe590aed74f2e4fc95271c62000fcda0e794c2b68fae361818db35ad80882201656ef145fd044da482c8198fa46aed7113c1 +MISC metadata.xml 595 SHA256 55b416d246753a1476c0880a8b8ee748248e207c618f07fe32c1640117382a61 SHA512 82d673d07781315d7c617f89f98d77e79e68304c6a6fb36f34546e53ad7b9eb81b1ca12a764f63423354f5d804d6cbfc39781d5310e6350b5e33d44cbf3d788a WHIRLPOOL cc76ebccabcf690b7781e8739da3b1788e59567da37bd31833e90a2c47190a7635855fd10138e8ef14251599b0a19dcea66e19b2fcefb7876d38d9b54ce7c0c4 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2 + +iEYEAREIAAYFAlT/aPwACgkQcaHudmEf86rZxACfQSPbefU2w1M+/tlcd4/hgqOD +3MwAnjgmp0P7mTXpSHywnXG9Te0wPVax +=Npqn +-----END PGP SIGNATURE----- diff --git a/dev-haskell/biosff/biosff-0.3.7.1.ebuild b/dev-haskell/biosff/biosff-0.3.7.1.ebuild new file mode 100644 index 000000000000..2bff9d66d9ed --- /dev/null +++ b/dev-haskell/biosff/biosff-0.3.7.1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/dev-haskell/biosff/biosff-0.3.7.1.ebuild,v 1.1 2015/03/10 21:58:41 slyfox Exp $ + +EAPI=5 + +# ebuild generated by hackport 0.3.4.9999 + +CABAL_FEATURES="bin lib profile haddock hoogle hscolour" +inherit haskell-cabal + +DESCRIPTION="Library and executables for working with SFF files" +HOMEPAGE="http://biohaskell.org/" +SRC_URI="mirror://hackage/packages/archive/${PN}/${PV}/${P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="+fclip +flower +frecover" + +RDEPEND="dev-haskell/binary:=[profile?] + >=dev-haskell/biocore-0.3:=[profile?] + dev-haskell/cmdargs:=[profile?] + >=dev-haskell/mtl-2:=[profile?] + >=dev-lang/ghc-7.4.1:= +" +DEPEND="${RDEPEND} + >=dev-haskell/cabal-1.6 +" + +src_configure() { + haskell-cabal_src_configure \ + $(cabal_flag fclip fclip) \ + $(cabal_flag flower flower) \ + $(cabal_flag frecover frecover) +} diff --git a/dev-haskell/biosff/metadata.xml b/dev-haskell/biosff/metadata.xml new file mode 100644 index 000000000000..714e2ad3539d --- /dev/null +++ b/dev-haskell/biosff/metadata.xml @@ -0,0 +1,15 @@ + + + + haskell + + The library contains the functionality for reading and writing + SFF files (sequencing data from 454 and Ion Torrent). It duplicates + code from (and is incompatible with) the "bio" library. + + + Build the fclip executable. + Build the flower executable. + Build the frecover executable. + + -- 2.26.2