From nobody Thu Feb 03 19:38:44 2022 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 C3C4A19A2205; Thu, 3 Feb 2022 19:38:44 +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 4JqTVr57wKz4vYP; Thu, 3 Feb 2022 19:38:44 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1643917124; 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=+/QEGOmpdYmCCy6X5hHZfLfkxdq07C9GySlEoWzqRzg=; b=erhtASseBllJuEBj9xQwxsraSwDKNpQxombZjjFFYEnsK2C8mRi0+DHY7r4KCllx7ABaPB gDotYhBx+uperSHHcv6kbzO4uUt0owzQbzzTS4tJu2pOLB+P//OQGcppMW3ZHCAkpxjCI/ 0aXFb2Qky0IQhXaP3g4SsOBpZ9WdrCgQUqEwUnEMzIsmbJkELZq9o9QjnkOJbDCFIQBsum SLSdiDIZ1s/V7Gkn3sqy7zWw3PZHierKSgtrTy9YrhV8F5skgXVHm2j1TA3Ck3FS9U7Ccq CnB+jIY8Mk6UK8xKulmbGI12UyMM7XDXEG0nXQHWCs55u4gjNLNcirin9ShB/g== 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 908621DDE6; Thu, 3 Feb 2022 19:38:44 +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 213JcirO042031; Thu, 3 Feb 2022 19:38:44 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 213JciA0042030; Thu, 3 Feb 2022 19:38:44 GMT (envelope-from git) Date: Thu, 3 Feb 2022 19:38:44 GMT Message-Id: <202202031938.213JciA0042030@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: d936c94c64a8 - main - biology/py-bcbio-gff: Read and write Generic Feature Format (GFF) 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: d936c94c64a84e88f8c9fbe350aa0445fda80a06 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1643917124; 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=+/QEGOmpdYmCCy6X5hHZfLfkxdq07C9GySlEoWzqRzg=; b=jQcSTKSQDwmR3jQ7FGB5a607LVgoGUx5/9u8eWa8096Bb/DduzKxuu3dkYVvnSQ719+A+c CHHS9wEQTpPnHP1bwZSHbs5TGgu6wdB1Y4UsTLaUYMid4pj98H7KzoWDvGB3wUt8xIPSp7 3nCAVK2cptMmneCm4043tBfX4cSaoQwfyG+Gocm/pCs9tbjPZo0xSd4QbVQdBVqdNfdmrR RKw7JSk96p+1ebcVmUAKojrp6AMzhizj7WeXfYVKrBOJ+D4fl7WcU2hP5Fh+rBxgfWt19P UoQXFubSpgzG7Y8ENg2ktmDm5NHJa7CBNprlolHw/lpnFgH9wl9QXkZSg+/nFw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1643917124; a=rsa-sha256; cv=none; b=cSkaaLpT92qPgRfITRAEb/Jv3TxggJdFyz2NLGayZ94aCww1lNxWjhcjdtN7QVxaBT+93w mwjejJZ4HkAo1hY3Zpa9BX1IYwuKSnMnn1C0iOJ/AkGl1evcmIy4NVdptNw1li+ad1TBSd iEkHnE3F6k86eGjf6ZL7GwkiPxQygnYIDY4hc7eS7a+KGwD7lFnTvTUnBzIL4dxKxiqZBW cr5iG3K445vSJgWCaSmzcHqLs5HT1EPgVjAAAFpAqZIarasYGSOnL6pP/cRZzJkN1KqVUh fjTDgN0Ozb2pkViGj9ukTC0dTTUoRepI3RGkdOAe7gCq8rfYcPYirHqQiRjx5g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=d936c94c64a84e88f8c9fbe350aa0445fda80a06 commit d936c94c64a84e88f8c9fbe350aa0445fda80a06 Author: Jason W. Bacon AuthorDate: 2022-02-03 19:37:21 +0000 Commit: Jason W. Bacon CommitDate: 2022-02-03 19:38:42 +0000 biology/py-bcbio-gff: Read and write Generic Feature Format (GFF) Read and write Generic Feature Format (GFF) with Biopython integration. Also adding py-dna-features-viewer to Makefile, missed on last commit --- biology/Makefile | 2 ++ biology/py-bcbio-gff/Makefile | 16 ++++++++++++++++ biology/py-bcbio-gff/distinfo | 3 +++ biology/py-bcbio-gff/pkg-descr | 3 +++ 4 files changed, 24 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 4e16a737f636..6712e8a40155 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -141,6 +141,7 @@ SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-PySCeS + SUBDIR += py-bcbio-gff SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python @@ -148,6 +149,7 @@ SUBDIR += py-cutadapt SUBDIR += py-deeptools SUBDIR += py-deeptoolsintervals + SUBDIR += py-dna-features-viewer SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils diff --git a/biology/py-bcbio-gff/Makefile b/biology/py-bcbio-gff/Makefile new file mode 100644 index 000000000000..b08f6d36f7f2 --- /dev/null +++ b/biology/py-bcbio-gff/Makefile @@ -0,0 +1,16 @@ +PORTNAME= bcbio-gff +DISTVERSION= 0.6.9 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Read and write Generic Feature Format (GFF) with Biopython integration + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= python +USE_PYTHON= autoplist distutils + +.include diff --git a/biology/py-bcbio-gff/distinfo b/biology/py-bcbio-gff/distinfo new file mode 100644 index 000000000000..72637728bd5c --- /dev/null +++ b/biology/py-bcbio-gff/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1643900022 +SHA256 (bcbio-gff-0.6.9.tar.gz) = 34dfa970e14f4533dc63c0a5512b7b5221e4a06449e6aaa344162ed5fdd7a1de +SIZE (bcbio-gff-0.6.9.tar.gz) = 44236 diff --git a/biology/py-bcbio-gff/pkg-descr b/biology/py-bcbio-gff/pkg-descr new file mode 100644 index 000000000000..2eec0e8e52a5 --- /dev/null +++ b/biology/py-bcbio-gff/pkg-descr @@ -0,0 +1,3 @@ +Read and write Generic Feature Format (GFF) with Biopython integration. + +WWW: https://pypi.python.org/project/bcbio-gff/