From nobody Sat Mar 19 12:26:39 2022 X-Original-To: dev-commits-ports-main@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 6FB8E1A26A5D; Sat, 19 Mar 2022 12:26:39 +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 4KLKqz2l6Lz50HT; Sat, 19 Mar 2022 12:26:39 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1647692799; 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=f7Qj7ga83P8e3pOdO13rSV1wst7EybpqhfkwethG3VQ=; b=w5AtcqIYgCOdk1kUISnWEeqq1sktunmfKB5Ek4AwMRAxDtWB904R3gniL4X4BZdh+stDUD r1QWs/pe+LEwwf3Roszout2E4dbyrzPCPDWLFVObQpQXRAoNNiAGpAD00n8hEWcknQ06+p IXcBXxemspCqxog3xPTn3ZE0iXYrCQnkDb85d8TEQ8xM+9pTSZfdFhj7ZS3S5+WFqNrIyK 2OzJoazPRGxX5ieJJHh7rhuMESJYAGElspA0QQf/jGzZJ4dQ4KtyC9lT4L4TAVqziEZf1q Fqapfw9y28kJjehhyGtwjgojpcBoo1od7a4mIvKxL2p1DzwEbzLAswUYcnZ1RQ== 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 3E036133C9; Sat, 19 Mar 2022 12:26:39 +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 22JCQdIG059834; Sat, 19 Mar 2022 12:26:39 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 22JCQdNo059833; Sat, 19 Mar 2022 12:26:39 GMT (envelope-from git) Date: Sat, 19 Mar 2022 12:26:39 GMT Message-Id: <202203191226.22JCQdNo059833@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: a47115b9cad4 - main - biology/fastq-trim: Lightening fast sequence read trimmer List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: a47115b9cad4784d5923f6a6e3d0fbef28623e8f Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1647692799; 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=f7Qj7ga83P8e3pOdO13rSV1wst7EybpqhfkwethG3VQ=; b=hw8GPqPu9dsFw0706EP/7YauvC3Xzjv9o2VqM1FmbVIQEcmdSn40nupTB5o5QCQ06by7gP P8esQ6aB0QuZ5xKmJqgyaeZ6ro4GlQ2XgCCU8jXi+NKy8Og/h1ND4qzbBpj+9EzGcs0KLu 1M50PspWnCCC7YlmZO09XxHIjiU7fb8A+pn2JHabj2MwUR6PceYDx3HkJUATG8wlLqDABr HNXDFSERUEZTuzGTGC9KAknpO2n3L1vbm93J2ulGhkqqmt9r4pPZe1G/YuO2dS9bdhuCnc 3sURhgpQdmBxhNUhe09KXtwm/DYCxHbqPHfj2zYVTeFJJBDl6wd6K7Q8W4u7AA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1647692799; a=rsa-sha256; cv=none; b=LbvUQraBV9X/1SP+pgJaWg663wvlagTh6yS5EGQwRy1/uvvU/GcBbfJxDJZxVo+ZZ38Q6D gZUtGAcP22V0oOb0sOug6UT317czDEMlC225640+eeZ06wr1WGx1trMe2oDGoUl6fB5Fjw mubsNU58gATBTdBBz6bSdqHOTjudLhrQx9KHHmOuB5tWAQIBr0poFztQ5JAemsamSeP11w D3Fjms7DScpv+42v2Pb28hSinLqiJOdfGJLkkHtqGnrUt4g2FOmrjz5xHxmvEUM8ulW2xJ m2jrqmghrc3kqcpWYVA0XtftJFPOtLnU5xUf5fpuDSlhsb9a9J643llpCgISmg== 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=a47115b9cad4784d5923f6a6e3d0fbef28623e8f commit a47115b9cad4784d5923f6a6e3d0fbef28623e8f Author: Jason W. Bacon AuthorDate: 2022-03-19 12:25:58 +0000 Commit: Jason W. Bacon CommitDate: 2022-03-19 12:25:58 +0000 biology/fastq-trim: Lightening fast sequence read trimmer Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads prior to analyses such as RNA-Seq. --- biology/Makefile | 1 + biology/fastq-trim/Makefile | 22 +++++++++++++ biology/fastq-trim/distinfo | 3 ++ biology/fastq-trim/pkg-descr | 4 +++ biology/fastq-trim/pkg-plist | 75 ++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 105 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 6712e8a40155..821cf358e8c3 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -45,6 +45,7 @@ SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp + SUBDIR += fastq-trim SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit diff --git a/biology/fastq-trim/Makefile b/biology/fastq-trim/Makefile new file mode 100644 index 000000000000..7b10097826ba --- /dev/null +++ b/biology/fastq-trim/Makefile @@ -0,0 +1,22 @@ +PORTNAME= fastq-trim +DISTVERSION= 0.1.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Lightening fast sequence read trimmer + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libbiolibc.so:biology/biolibc libxtend.so:devel/libxtend + +USE_GITHUB= yes + +GH_ACCOUNT= outpaddling + +MAKE_ENV= VERSION=${PORTVERSION} + +pre-build: + (cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend) + +.include diff --git a/biology/fastq-trim/distinfo b/biology/fastq-trim/distinfo new file mode 100644 index 000000000000..8b2366479432 --- /dev/null +++ b/biology/fastq-trim/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1647691961 +SHA256 (outpaddling-fastq-trim-0.1.1_GH0.tar.gz) = ce959484b823f20a5e6e3c493490e71183865d15b6023ee7dc3a5822cc6b176c +SIZE (outpaddling-fastq-trim-0.1.1_GH0.tar.gz) = 30087 diff --git a/biology/fastq-trim/pkg-descr b/biology/fastq-trim/pkg-descr new file mode 100644 index 000000000000..e3ec0de0561a --- /dev/null +++ b/biology/fastq-trim/pkg-descr @@ -0,0 +1,4 @@ +Fastq-trim is a hopefully lightening fast read trimming tool for QA of +DNA and RNA reads prior to analyses such as RNA-Seq. + +WWW: https://github.com/outpaddling/Fastq-trim diff --git a/biology/fastq-trim/pkg-plist b/biology/fastq-trim/pkg-plist new file mode 100644 index 000000000000..4c55bfdd58f8 --- /dev/null +++ b/biology/fastq-trim/pkg-plist @@ -0,0 +1,75 @@ +bin/fastq-trim +bin/fastq-vis +include/fastq-trim-accessors.h +include/fastq-trim-mutators.h +include/fastq-trim-rvs.h +include/fastq-trim.h +lib/libfastq-trim.a +man/man1/fastq-trim.1.gz +man/man1/fastq-vis.1.gz +man/man3/FASTQ_TRIM_ADAPTER1.3.gz +man/man3/FASTQ_TRIM_ADAPTER1_AE.3.gz +man/man3/FASTQ_TRIM_ADAPTER2.3.gz +man/man3/FASTQ_TRIM_ADAPTER2_AE.3.gz +man/man3/FASTQ_TRIM_ADAPTER_MATCH_FUNCTION.3.gz +man/man3/FASTQ_TRIM_INFILE1.3.gz +man/man3/FASTQ_TRIM_INFILE1_AE.3.gz +man/man3/FASTQ_TRIM_INFILE2.3.gz +man/man3/FASTQ_TRIM_INFILE2_AE.3.gz +man/man3/FASTQ_TRIM_INSTREAM1.3.gz +man/man3/FASTQ_TRIM_INSTREAM1_AE.3.gz +man/man3/FASTQ_TRIM_INSTREAM2.3.gz +man/man3/FASTQ_TRIM_INSTREAM2_AE.3.gz +man/man3/FASTQ_TRIM_MAX_MISMATCH_PERCENT.3.gz +man/man3/FASTQ_TRIM_MIN_LENGTH.3.gz +man/man3/FASTQ_TRIM_MIN_MATCH.3.gz +man/man3/FASTQ_TRIM_MIN_QUAL.3.gz +man/man3/FASTQ_TRIM_OUTFILE1.3.gz +man/man3/FASTQ_TRIM_OUTFILE1_AE.3.gz +man/man3/FASTQ_TRIM_OUTFILE2.3.gz +man/man3/FASTQ_TRIM_OUTFILE2_AE.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM1.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM1_AE.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM2.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM2_AE.3.gz +man/man3/FASTQ_TRIM_PHRED_BASE.3.gz +man/man3/FASTQ_TRIM_POLYA_MIN_LEN.3.gz +man/man3/FASTQ_TRIM_VERBOSE.3.gz +man/man3/fastq_trim_set_adapter1.3.gz +man/man3/fastq_trim_set_adapter1_ae.3.gz +man/man3/fastq_trim_set_adapter1_cpy.3.gz +man/man3/fastq_trim_set_adapter2.3.gz +man/man3/fastq_trim_set_adapter2_ae.3.gz +man/man3/fastq_trim_set_adapter2_cpy.3.gz +man/man3/fastq_trim_set_adapter_match_function.3.gz +man/man3/fastq_trim_set_infile1.3.gz +man/man3/fastq_trim_set_infile1_ae.3.gz +man/man3/fastq_trim_set_infile1_cpy.3.gz +man/man3/fastq_trim_set_infile2.3.gz +man/man3/fastq_trim_set_infile2_ae.3.gz +man/man3/fastq_trim_set_infile2_cpy.3.gz +man/man3/fastq_trim_set_instream1.3.gz +man/man3/fastq_trim_set_instream1_ae.3.gz +man/man3/fastq_trim_set_instream1_cpy.3.gz +man/man3/fastq_trim_set_instream2.3.gz +man/man3/fastq_trim_set_instream2_ae.3.gz +man/man3/fastq_trim_set_instream2_cpy.3.gz +man/man3/fastq_trim_set_max_mismatch_percent.3.gz +man/man3/fastq_trim_set_min_length.3.gz +man/man3/fastq_trim_set_min_match.3.gz +man/man3/fastq_trim_set_min_qual.3.gz +man/man3/fastq_trim_set_outfile1.3.gz +man/man3/fastq_trim_set_outfile1_ae.3.gz +man/man3/fastq_trim_set_outfile1_cpy.3.gz +man/man3/fastq_trim_set_outfile2.3.gz +man/man3/fastq_trim_set_outfile2_ae.3.gz +man/man3/fastq_trim_set_outfile2_cpy.3.gz +man/man3/fastq_trim_set_outstream1.3.gz +man/man3/fastq_trim_set_outstream1_ae.3.gz +man/man3/fastq_trim_set_outstream1_cpy.3.gz +man/man3/fastq_trim_set_outstream2.3.gz +man/man3/fastq_trim_set_outstream2_ae.3.gz +man/man3/fastq_trim_set_outstream2_cpy.3.gz +man/man3/fastq_trim_set_phred_base.3.gz +man/man3/fastq_trim_set_polya_min_len.3.gz +man/man3/fastq_trim_set_verbose.3.gz