diff options
Diffstat (limited to 'sci-biology/abyss')
| -rw-r--r-- | sci-biology/abyss/Manifest | 5 | ||||
| -rw-r--r-- | sci-biology/abyss/abyss-2.0.2-r1.ebuild | 55 | ||||
| -rw-r--r-- | sci-biology/abyss/metadata.xml | 18 |
3 files changed, 78 insertions, 0 deletions
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest new file mode 100644 index 000000000000..53cbd51fdb65 --- /dev/null +++ b/sci-biology/abyss/Manifest @@ -0,0 +1,5 @@ +DIST abyss-2.0.2.tar.gz 1036135 SHA256 6482b81eb5439703c0dbf6cd7ac25cd0df7541d9e04ef7865343b241e21db460 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 WHIRLPOOL 23447cb00b0bb9b5b8a724ba44f8d7193d9640ccd19956b42bbbd83b67557b66b7c68141d6f292c4ab11ab523286471d5ee1c938f22749a61162de056a0d903e +EBUILD abyss-2.0.2-r1.ebuild 1255 SHA256 76cd126c146ca100d00fe6b48b8a9a2bfcdef7db9dabfcb7ab6eccbeaa3d7c68 SHA512 2a75296cc2d5884be09ce2aa6280af3e54735501125da0dea4cbd297f18061a94ac1ced98990087c209f196c8f624b4cae24c7f7c383913b59ba0c51e9823ed9 WHIRLPOOL d50d12d60d22f98d320a42693de9eef945d64067ac0b5cf25cfc24b8b657789b04b8e08c9ab133a3683b0486b8d0441ec35d2c7d24eb1f2930e78ca152d84d2f +MISC ChangeLog 5076 SHA256 033515486551f430c662c0f8f24932c83fbd40ce3dc20fc487aad8b2449d93e3 SHA512 b16c9e47c2af4c8dcdf421f487aa4d665b3658457fc77a19f41bc62b7d12df756f7fd0d5c0ff2e03b0c3dd4558414126be15c0c6e9cff10d06c4e1e45871bb21 WHIRLPOOL 45db002d9a6e585df0460ab09fd046d6dab8cda26a81aba849793ed1d0c54ce13330b7963274d633410934d6f7d6c405a91f145c33239afb6082fe865449288e +MISC ChangeLog-2015 3086 SHA256 3e295bd3a13f20016e1baaf773c888fad647ad1aa09f77719590a3d01b33e320 SHA512 28de3b6bb48d775fb1ecd1bcc37aadf43451a7200ce691b11833a41dcdde6046e70e7a3b76d5fecb2cadcd96fd94d3e67b6ad1758b9132028aac19339c8e9bd4 WHIRLPOOL 9d73031727499d87e932b55833512068e36c57ca6ab4dc06d8a458f3db89fefda263d858d322468f6de5a9a34113f1a826a01878c633d19ed3d79d962ba410ff +MISC metadata.xml 572 SHA256 5649b00a9f038a5916a2205b92cf55df64d886a7451362d2ad481d09dd53f412 SHA512 b7461a55a1f34d22b8faceb40c15f66d7564a5fd3ccd626533972f25fcca36f8ce47e7edc5e96e7eab6c9bfc27ac4e094b419c241b7cc4de051025e1a9522198 WHIRLPOOL cd121dd5eeb4084400bc72b6c9af38076b064d5f12b19fe7964a592fdd881fd1bafd4cd8a2389d9ba5a03a99762452e2f53d7898916b09e258692d24a23a24c9 diff --git a/sci-biology/abyss/abyss-2.0.2-r1.ebuild b/sci-biology/abyss/abyss-2.0.2-r1.ebuild new file mode 100644 index 000000000000..0d1c14ac265e --- /dev/null +++ b/sci-biology/abyss/abyss-2.0.2-r1.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost:= + misc-haskell? ( + dev-libs/gmp:0= + virtual/libffi:0= + ) + mpi? ( sys-cluster/openmpi )" +DEPEND="${RDEPEND} + misc-haskell? ( + dev-lang/ghc + dev-haskell/mmap + )" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +src_prepare() { + default + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + # disable building haskell tool Misc/samtobreak + # unless request by user: bug #534412 + use misc-haskell || export ac_cv_prog_ac_ct_GHC= + + econf $(use_enable openmp) +} diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml new file mode 100644 index 000000000000..47116e507d89 --- /dev/null +++ b/sci-biology/abyss/metadata.xml @@ -0,0 +1,18 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="project"> + <email>haskell@gentoo.org</email> + <name>Gentoo Haskell</name> + </maintainer> + <use> + <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> + </use> + <upstream> + <remote-id type="github">bcgsc/abyss</remote-id> + </upstream> +</pkgmetadata> |