From owner-dev-commits-ports-all@freebsd.org Mon Apr 12 23:38:10 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id D86C85E2128; Mon, 12 Apr 2021 23:38:10 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FK4tB5mT7z3HjN; Mon, 12 Apr 2021 23:38:10 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id B8D6E2051E; Mon, 12 Apr 2021 23:38:10 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 13CNcArn029945; Mon, 12 Apr 2021 23:38:10 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 13CNcAbA029944; Mon, 12 Apr 2021 23:38:10 GMT (envelope-from git) Date: Mon, 12 Apr 2021 23:38:10 GMT Message-Id: <202104122338.13CNcAbA029944@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 912872756265 - main - biology/py-crossmap: Lift over genomics coordinates between assemblies MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 9128727562651ebcc304714cccd03d9643165a74 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 12 Apr 2021 23:38:10 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=9128727562651ebcc304714cccd03d9643165a74 commit 9128727562651ebcc304714cccd03d9643165a74 Author: Jason W. Bacon AuthorDate: 2021-04-12 23:30:30 +0000 Commit: Jason W. Bacon CommitDate: 2021-04-12 23:37:51 +0000 biology/py-crossmap: Lift over genomics coordinates between assemblies CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF. --- biology/Makefile | 1 + biology/py-crossmap/Makefile | 21 +++++++++++++++++++++ biology/py-crossmap/distinfo | 3 +++ .../py-crossmap/files/patch-lib_cmmodule_twoList.py | 18 ++++++++++++++++++ biology/py-crossmap/files/patch-setup.py | 10 ++++++++++ biology/py-crossmap/pkg-descr | 6 ++++++ 6 files changed, 59 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 25eba238a6ad..606e1982ee9b 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -127,6 +127,7 @@ SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python + SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 diff --git a/biology/py-crossmap/Makefile b/biology/py-crossmap/Makefile new file mode 100644 index 000000000000..7946de949b5e --- /dev/null +++ b/biology/py-crossmap/Makefile @@ -0,0 +1,21 @@ +PORTNAME= crossmap +DISTVERSION= 0.5.2 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= CrossMap-${DISTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Lift over genomics coordinates between assemblies + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}bx-python>0:biology/py-bx-python@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pyBigWig>0:biology/py-bigwig@${PY_FLAVOR} + +USES= python:3.5+ +USE_PYTHON= autoplist cython distutils + +.include diff --git a/biology/py-crossmap/distinfo b/biology/py-crossmap/distinfo new file mode 100644 index 000000000000..e78c67b1ddcf --- /dev/null +++ b/biology/py-crossmap/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1617575391 +SHA256 (CrossMap-0.5.2.tar.gz) = d996c7a17ca2665903d7bfa4ca67d35c37c800e1ce3129ed1274e65504b93d69 +SIZE (CrossMap-0.5.2.tar.gz) = 10866811 diff --git a/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py b/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py new file mode 100644 index 000000000000..efbb0c474374 --- /dev/null +++ b/biology/py-crossmap/files/patch-lib_cmmodule_twoList.py @@ -0,0 +1,18 @@ +--- lib/cmmodule/twoList.py.orig 2021-04-04 22:42:53 UTC ++++ lib/cmmodule/twoList.py +@@ -5,7 +5,7 @@ from operator import mul,add,sub + def check_list(v1,v2): + '''check if the length of two list is same''' + if v1.size != v2.size: +- raise ValueError,"the lenght of both arrays must be the same" ++ raise ValueError("the length of both arrays must be the same") + pass + + def Add(v1,v2): +@@ -50,4 +50,4 @@ def Min(v1,v2): + def euclidean_distance(v1,v2): + '''return euclidean distance''' + check_list(v1,v2) +- return (sum((v1.__sub__(v2))**2) / v1.size)**0.5 +\ No newline at end of file ++ return (sum((v1.__sub__(v2))**2) / v1.size)**0.5 diff --git a/biology/py-crossmap/files/patch-setup.py b/biology/py-crossmap/files/patch-setup.py new file mode 100644 index 000000000000..4fa46ca7cc20 --- /dev/null +++ b/biology/py-crossmap/files/patch-setup.py @@ -0,0 +1,10 @@ +--- setup.py.orig 2021-04-05 15:27:07 UTC ++++ setup.py +@@ -11,7 +11,6 @@ def main(): + setup( name = "CrossMap", + version = "0.5.2", + python_requires='>=3.5', +- py_modules = [ 'psyco_full' ], + packages = find_packages( 'lib' ), + package_dir = { '': 'lib' }, + package_data = { '': ['*.ps'] }, diff --git a/biology/py-crossmap/pkg-descr b/biology/py-crossmap/pkg-descr new file mode 100644 index 000000000000..dfb768a40775 --- /dev/null +++ b/biology/py-crossmap/pkg-descr @@ -0,0 +1,6 @@ +CrossMap is a program for genome coordinates conversion between different +assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used +file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, +and gVCF. + +WWW: https://pypi.python.org/pypi/crossmap