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Fri, 7 Dec 2018 00:26:05 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id wB70Q44B073181; Fri, 7 Dec 2018 00:26:04 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201812070026.wB70Q44B073181@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Fri, 7 Dec 2018 00:26:04 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r486814 - in head/biology: . checkm X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . checkm X-SVN-Commit-Revision: 486814 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 7EDA96E310 X-Spamd-Result: default: False [-1.88 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-0.87)[-0.865,0]; NEURAL_HAM_SHORT(-0.96)[-0.958,0]; NEURAL_HAM_LONG(-0.05)[-0.054,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-Rspamd-Server: mx1.freebsd.org X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 07 Dec 2018 00:26:06 -0000 Author: yuri Date: Fri Dec 7 00:26:04 2018 New Revision: 486814 URL: https://svnweb.freebsd.org/changeset/ports/486814 Log: New port: math/checkm: Quality assessment tool for the microbial genomes Added: head/biology/checkm/ head/biology/checkm/Makefile (contents, props changed) head/biology/checkm/distinfo (contents, props changed) head/biology/checkm/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Dec 7 00:12:55 2018 (r486813) +++ head/biology/Makefile Fri Dec 7 00:26:04 2018 (r486814) @@ -16,6 +16,7 @@ SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta + SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw Added: head/biology/checkm/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/checkm/Makefile Fri Dec 7 00:26:04 2018 (r486814) @@ -0,0 +1,27 @@ +# $FreeBSD$ + +PORTNAME= CheckM +DISTVERSIONPREFIX= v +DISTVERSION= 1.0.12 +CATEGORIES= biology python + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Quality assessment tool for the microbial genomes + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}DendroPy>=4.0.0:science/py-DendroPy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.3.1:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pysam>=0.8.3:biology/py-pysam@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=0.9.0:science/py-scipy@${PY_FLAVOR} + +USES= python +USE_GITHUB= yes +GH_ACCOUNT= Ecogenomics +USE_PYTHON= distutils noflavors autoplist + +NO_ARCH= yes + +.include Added: head/biology/checkm/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/checkm/distinfo Fri Dec 7 00:26:04 2018 (r486814) @@ -0,0 +1,3 @@ +TIMESTAMP = 1544141583 +SHA256 (Ecogenomics-CheckM-v1.0.12_GH0.tar.gz) = 4aca26d0ae903ed7567cfc6ec53dc1d2ea909d58a0c4c6e2318a1885abbcfd91 +SIZE (Ecogenomics-CheckM-v1.0.12_GH0.tar.gz) = 211396 Added: head/biology/checkm/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/checkm/pkg-descr Fri Dec 7 00:26:04 2018 (r486814) @@ -0,0 +1,12 @@ +CheckM provides a set of tools for assessing the quality of genomes recovered +from isolates, single cells, or metagenomes. It provides robust estimates of +genome completeness and contamination by using collocated sets of genes that +are ubiquitous and single-copy within a phylogenetic lineage. Assessment of +genome quality can also be examined using plots depicting key genomic +characteristics (e.g., GC, coding density) which highlight sequences outside +the expected distributions of a typical genome. CheckM also provides tools for +identifying genome bins that are likely candidates for merging based on marker +set compatibility, similarity in genomic characteristics, and proximity within +a reference genome tree. + +WWW: https://ecogenomics.github.io/CheckM/