From nobody Fri Jul 28 15:42:40 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4RCBjF0xk0z4pnxw; Fri, 28 Jul 2023 15:42:41 +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 4RCBjF0XTjz3D6j; Fri, 28 Jul 2023 15:42:41 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1690558961; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=M4xDCslbhMHH3Ve2pt+Bfr7TOXyugQKax490ZyeCG5E=; b=YKCNOSxmHjQ+KIBhNf4H2Ea7j3o+Xc2r+08Q3TsdLTsOjitz8Vn048oeSkfI1XEBT9/OBC lxABZXVRsmbva1udVu+ir8m1ceiO4P+/XXlt8lpE9vxQ6xLtv9QRFJXNYBlwTW0guvgda9 90R2qavgSbonlQ/pw3uJBooCARybr5fF21VIsjbAGDMeUXRifJo3DybXgCqQGhoyGseSiQ KcGIZAuq9iBZbyGpNPB+13XynokwbgmkuRfXjkFtsaDXeQWzhTs27ayS+3xynutyBqGt6r SamvpSNRTVPVs9MpLHmJ+1jiKVjy94uhYGjdDtOAPSl+pSliLoMyaUuH4+5U5A== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1690558961; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=M4xDCslbhMHH3Ve2pt+Bfr7TOXyugQKax490ZyeCG5E=; b=VOsmIPbppvEt5phHr1NaMZB+aCMtjFxJf03kh5FtwlBuT6Q/geOpb3aCIX4e1OkYQsWHax Cd8DyzDBlTVTPcziUlSf1G+dgzG12eP5r63SAX5gNPXzIy+PjcgJkdjOcr110IyeEJeB8o qmYyzU77zZHM/CUUof6JF9yhUTRJmzLBreapmfzYyZgm5CZMAfcn1kjCR3uW2KlXlOVr9M Oz10qdDkXm1VIpIBQrQXtfSP5ikXPjE70aG3e+x37lrSpy3k6whmLNnxUe20MxXJmQ2KqC MubcTYIo6SiaEB5FvNy453jt3jKD4yDO9q3nD78nWwjza8I8uLZBAIaG2t4Gyg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1690558961; a=rsa-sha256; cv=none; b=VuXw0yJy9P0Um3ANN7xrgexT4rSd/+Qb7c+wktsID4tcWQpWYq62l2wNCPr8MA+sG0z8n5 i8OqDd84CmoLCiwdCDIsDM0XvKM1qXC9cYHC68rr37RLGfdu/U/kIMxGJUJgcgGFF6bQZm 8dhxtxTbMNmvHgz7pCi03FTEKeJ3rvRlZYloO61d/BEgVyyxHOQfMN1AlTeen+n3ouklkF lIzba8N/h3gzNjFFtfTCGdN/U4729yFS4L/Ds/pMRN760v91SIiTck3we0dQc2AdXgfDxM EYhcQDm5+n3eORIqpL5sYEKp8V1cM1fFCUclyBXxio2NHZ6xFvmTopPftoSCzg== 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 4RCBjD6j4lzwgt; Fri, 28 Jul 2023 15:42:40 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 36SFgeJU025463; Fri, 28 Jul 2023 15:42:40 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 36SFgeM1025462; Fri, 28 Jul 2023 15:42:40 GMT (envelope-from git) Date: Fri, 28 Jul 2023 15:42:40 GMT Message-Id: <202307281542.36SFgeM1025462@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: 505bb0df2b00 - main - biology/py-htseq: Python library for sequence analysis 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: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 505bb0df2b00b2e9a65545764cf39855eab6bfa5 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=505bb0df2b00b2e9a65545764cf39855eab6bfa5 commit 505bb0df2b00b2e9a65545764cf39855eab6bfa5 Author: Jason W. Bacon AuthorDate: 2023-07-28 15:41:58 +0000 Commit: Jason W. Bacon CommitDate: 2023-07-28 15:41:58 +0000 biology/py-htseq: Python library for sequence analysis HTSeq is a Python library to facilitate programmatic analysis of data from high-throughput sequencing (HTS) experiments. A popular component of HTSeq is htseq-count, a script to quantify gene expression in bulk and single-cell RNA-Seq and similar experiments. --- biology/Makefile | 1 + biology/py-htseq/Makefile | 30 ++++++++++++++++++++++++++++++ biology/py-htseq/distinfo | 3 +++ biology/py-htseq/pkg-descr | 4 ++++ 4 files changed, 38 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index ecb49b10cc6c..dc020b1fd61e 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -171,6 +171,7 @@ SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits + SUBDIR += py-htseq SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy diff --git a/biology/py-htseq/Makefile b/biology/py-htseq/Makefile new file mode 100644 index 000000000000..2c5ff14011da --- /dev/null +++ b/biology/py-htseq/Makefile @@ -0,0 +1,30 @@ +PORTNAME= HTSeq +DISTVERSION= 2.0.3 +CATEGORIES= biology python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Python library to facilitate programmatic analysis of sequence data +WWW= https://pypi.python.org/project/htseq/ + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ + ${PKGNAMEPREFIX}matplotlib>=1.4.3:math/py-matplotlib@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}scipy>1.5.0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.1.0:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.4:math/py-matplotlib@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist cython distutils pytest + +post-stage: + ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/HTSeq/_StepVector.cpython-39.so + ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/HTSeq/_HTSeq.cpython-39.so + +.include diff --git a/biology/py-htseq/distinfo b/biology/py-htseq/distinfo new file mode 100644 index 000000000000..88554006d541 --- /dev/null +++ b/biology/py-htseq/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1690498174 +SHA256 (HTSeq-2.0.3.tar.gz) = c7e7eb29bdc44e80d2d68e3599fa8a8f1d9d6475624dcf1b9644285a8a9c0fac +SIZE (HTSeq-2.0.3.tar.gz) = 394178 diff --git a/biology/py-htseq/pkg-descr b/biology/py-htseq/pkg-descr new file mode 100644 index 000000000000..afafda9c12f4 --- /dev/null +++ b/biology/py-htseq/pkg-descr @@ -0,0 +1,4 @@ +HTSeq is a Python library to facilitate programmatic analysis of data +from high-throughput sequencing (HTS) experiments. A popular component +of HTSeq is htseq-count, a script to quantify gene expression in bulk +and single-cell RNA-Seq and similar experiments.