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Sat, 26 Nov 2022 11:17:24 GMT (envelope-from git) Date: Sat, 26 Nov 2022 11:17:24 GMT Message-Id: <202211261117.2AQBHOtt070790@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: affc6502d525 - main - biology/metaeuk: New port: Gene discovery and annotation for large-scale eukaryotic metagenomics List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: affc6502d525205e07e5770118a8dc8577bb7d1d Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=affc6502d525205e07e5770118a8dc8577bb7d1d commit affc6502d525205e07e5770118a8dc8577bb7d1d Author: Yuri Victorovich AuthorDate: 2022-11-26 01:46:14 +0000 Commit: Yuri Victorovich CommitDate: 2022-11-26 11:04:46 +0000 biology/metaeuk: New port: Gene discovery and annotation for large-scale eukaryotic metagenomics --- biology/Makefile | 1 + biology/metaeuk/Makefile | 31 +++++++++++++++++++++++++++++++ biology/metaeuk/distinfo | 7 +++++++ biology/metaeuk/pkg-descr | 8 ++++++++ 4 files changed, 47 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index fc30f158d16a..98b1f2663190 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -93,6 +93,7 @@ SUBDIR += mafft SUBDIR += mapm3 SUBDIR += megahit + SUBDIR += metaeuk SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 diff --git a/biology/metaeuk/Makefile b/biology/metaeuk/Makefile new file mode 100644 index 000000000000..dd7010c29c00 --- /dev/null +++ b/biology/metaeuk/Makefile @@ -0,0 +1,31 @@ +PORTNAME= metaeuk +DISTVERSION= 6 +DISTVERSIONSUFFIX= -a5d39d9 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Gene discovery and annotation for large-scale eukaryotic metagenomics +WWW= https://github.com/soedinglab/metaeuk + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENCE.md + +BUILD_DEPENDS= xxd:editors/vim +TEST_DEPENDS= bash:shells/bash + +USES= cmake perl5 shebangfix +USE_PERL5= build + +USE_GITHUB= yes +GH_ACCOUNT= soedinglab +GH_TUPLE= soedinglab:metaeuk-regression:6404519:metaeuk_regression/tests \ + soedinglab:MMseqs2-Regression:f69b185:MMseqs2_Regression/lib/mmseqs/util/regression + +SHEBANG_GLOB= *.sh + +PLIST_FILES= bin/metaeuk + +do-test: + @cd ${WRKSRC}/tests && ./run.sh ${STAGEDIR}${PREFIX}/bin/metaeuk + +.include diff --git a/biology/metaeuk/distinfo b/biology/metaeuk/distinfo new file mode 100644 index 000000000000..cb642b65977d --- /dev/null +++ b/biology/metaeuk/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1669423980 +SHA256 (soedinglab-metaeuk-6-a5d39d9_GH0.tar.gz) = be19c26f5bdb7dcdd7bc48172105afecf19e5a2e5555edb3ba0c4aa0e4aac126 +SIZE (soedinglab-metaeuk-6-a5d39d9_GH0.tar.gz) = 13145257 +SHA256 (soedinglab-metaeuk-regression-6404519_GH0.tar.gz) = 5ac6c7438dc23374de5304564020e13ee7a6af99e60495083d74a5a272719b4d +SIZE (soedinglab-metaeuk-regression-6404519_GH0.tar.gz) = 6719192 +SHA256 (soedinglab-MMseqs2-Regression-f69b185_GH0.tar.gz) = 3774e16182cf8ce33d83c8c5170a57ebcec1ba137318d4762a89fd25c2890e78 +SIZE (soedinglab-MMseqs2-Regression-f69b185_GH0.tar.gz) = 27714150 diff --git a/biology/metaeuk/pkg-descr b/biology/metaeuk/pkg-descr new file mode 100644 index 000000000000..2ab6502d6c02 --- /dev/null +++ b/biology/metaeuk/pkg-descr @@ -0,0 +1,8 @@ +MetaEuk is a modular toolkit designed for large-scale gene discovery and +annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and +sensitive homology search capabilities of MMseqs2 with a dynamic programming +procedure to recover optimal exons sets. It reduces redundancies in multiple +discoveries of the same gene and resolves conflicting gene predictions on the +same strand. MetaEuk is GPLv3-licensed open source software that is implemented +in C++ and available for Linux and macOS. The software is designed to run +efficiently on multiple cores.