A bioinformatics library for haskell (requested by Martin MOKREJŠ).

Package-Manager: portage-2.2.17/cvs/Linux x86_64
Manifest-Sign-Key: 0x611FF3AA

diff --git a/dev-haskell/biocore/ChangeLog b/dev-haskell/biocore/ChangeLog
new file mode 100644 (file)
index 0000000..413e1bc
--- /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 <slyfox@gentoo.org> +biocore-0.3.1.ebuild,
+  +metadata.xml:
+  A bioinformatics library for haskell (requested by Martin MOKREJŠ).

diff --git a/dev-haskell/biocore/Manifest b/dev-haskell/biocore/Manifest
new file mode 100644 (file)
index 0000000..4cb40db
--- /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
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+-----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 (file)
index 0000000..17684df
--- /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 (file)
index 0000000..738abba
--- /dev/null
+++ b/dev-haskell/biocore/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+       <herd>haskell</herd>
+       <longdescription>
+               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.
+       </longdescription>
+</pkgmetadata>

diff --git a/dev-haskell/biofasta/ChangeLog b/dev-haskell/biofasta/ChangeLog
new file mode 100644 (file)
index 0000000..efb7bcd
--- /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 <slyfox@gentoo.org> +biofasta-0.0.3.ebuild,
+  +metadata.xml:
+  A bioinformatics library for haskell (requested by Martin MOKREJŠ).

diff --git a/dev-haskell/biofasta/Manifest b/dev-haskell/biofasta/Manifest
new file mode 100644 (file)
index 0000000..27a76de
--- /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
+
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+=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 (file)
index 0000000..06abeb7
--- /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 (file)
index 0000000..e2d400a
--- /dev/null
+++ b/dev-haskell/biofasta/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+       <herd>haskell</herd>
+       <longdescription>
+               Library for reading fasta sequence files
+       </longdescription>
+</pkgmetadata>

diff --git a/dev-haskell/biosff/ChangeLog b/dev-haskell/biosff/ChangeLog
new file mode 100644 (file)
index 0000000..7fa79a6
--- /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 <slyfox@gentoo.org> +biosff-0.3.7.1.ebuild,
+  +metadata.xml:
+  A bioinformatics library for haskell (requested by Martin MOKREJŠ).

diff --git a/dev-haskell/biosff/Manifest b/dev-haskell/biosff/Manifest
new file mode 100644 (file)
index 0000000..9f28a9f
--- /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
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+Version: GnuPG v2
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+-----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 (file)
index 0000000..2bff9d6
--- /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 (file)
index 0000000..714e2ad
--- /dev/null
+++ b/dev-haskell/biosff/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+       <herd>haskell</herd>
+       <longdescription>
+               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 &quot;bio&quot; library.
+       </longdescription>
+       <use>
+               <flag name="fclip">Build the fclip executable.</flag>
+               <flag name="flower">Build the flower executable.</flag>
+               <flag name="frecover">Build the frecover executable.</flag>
+       </use>
+</pkgmetadata>