Date: Wed, 26 May 2021 22:25:25 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5b018ca96217 - main - biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit Message-ID: <202105262225.14QMPPFV001232@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=5b018ca96217b47530cb3e48dd6f869be279ebaa commit 5b018ca96217b47530cb3e48dd6f869be279ebaa Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-05-26 21:49:16 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-05-26 22:25:22 +0000 biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit --- biology/Makefile | 1 + biology/taxonkit/Makefile | 19 +++++++++++++++++++ biology/taxonkit/distinfo | 5 +++++ biology/taxonkit/pkg-descr | 10 ++++++++++ 4 files changed, 35 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 38761df9c785..4025c269aef3 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -179,6 +179,7 @@ SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp + SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile new file mode 100644 index 000000000000..305f8f97e3fc --- /dev/null +++ b/biology/taxonkit/Makefile @@ -0,0 +1,19 @@ +PORTNAME= taxonkit +DISTVERSIONPREFIX= v +DISTVERSION= 0.8.0 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Practical and efficient NCBI taxonomy toolkit + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= go:modules + +GO_MODULE= github.com/shenwei356/taxonkit +GO_TARGET= ./${PORTNAME} + +PLIST_FILES= bin/${PORTNAME} + +.include <bsd.port.mk> diff --git a/biology/taxonkit/distinfo b/biology/taxonkit/distinfo new file mode 100644 index 000000000000..a85f4e8a9b3c --- /dev/null +++ b/biology/taxonkit/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1622065223 +SHA256 (go/biology_taxonkit/taxonkit-v0.8.0/v0.8.0.mod) = 9fb5139703523fd06f121e31ae420b1262ac437be1e25a0c8410c0ffa8291987 +SIZE (go/biology_taxonkit/taxonkit-v0.8.0/v0.8.0.mod) = 507 +SHA256 (go/biology_taxonkit/taxonkit-v0.8.0/v0.8.0.zip) = 087b47ad82fa3318aedb6954abdadc5d8637f07c43c4037e1b9b825214353833 +SIZE (go/biology_taxonkit/taxonkit-v0.8.0/v0.8.0.zip) = 1494298 diff --git a/biology/taxonkit/pkg-descr b/biology/taxonkit/pkg-descr new file mode 100644 index 000000000000..4bec18ee74e9 --- /dev/null +++ b/biology/taxonkit/pkg-descr @@ -0,0 +1,10 @@ +TaxonKit allows to: +* list taxonomic subtrees (TaxIds) +* query taxonomic lineage of given TaxIds +* reformat lineage in canonical ranks +* convert scientific names to TaxIds +* filter TaxIds by taxonomic rank range +* compute lowest common ancestor (LCA) for TaxIds +* create TaxId changelog from dump archives + +WWW: https://bioinf.shenwei.me/taxonkit/
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