From nobody Thu Oct 24 13:32:33 2024 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 4XZ6KY32Jzz5bSYc; Thu, 24 Oct 2024 13:32:33 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XZ6KY1tFzz4BNn; Thu, 24 Oct 2024 13:32:33 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1729776753; 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=vtYHOYEt8hcGh+629JyvqpP1Y3c8KeteUMeO2QMryss=; b=C4oq2SesSgCAqoZusQYpvRPnVAzqOVVZ7bN1LCkv5Nr39X8Vybuy6qpgh8eRLoDwMjojyn auOvFopK9K5UQ3PKl9F7kpt5Ax+ntbgWyo/qXGcqokKcggTaaWdgRv6LfrXlxsohIVnPQZ jlwrjfzta0a6wdQI0QTHauxI8gBppuIfQTvcjfUiai3sFBqC1VQBIQGRiXOptSeUQ55U3U kymRaZvTUtmb62nKw+9VWwa4Iv3CVreHVfnLEaaHwacIKWcW+NAtPplzeWGxq0+xTkXqqu U7PN0DVwMqrnPu7r9pLYvF4u5zWP4vAqXfkhhfONsJtQYq/tczm57pUPrNnamQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1729776753; 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=vtYHOYEt8hcGh+629JyvqpP1Y3c8KeteUMeO2QMryss=; b=c+uxDrgc0l06Uij0pGgBRTvOhriI7SdZx4ei2sbGzFeMesBwPELGrK05stYJxBCKDIyaei +7L2fdBuFMjAj9P++DA8yk9InyqCGg2s03PNjY8GdyFyfrC4pzNPX0AhxEC7e/Jupbqa4B LdFqChYVP+sdXr1Vq6AFFp4Z8JPTlZC/3VrQgPZGUfYryyO+jSDNhs7gH60SCNKuWGsI5r elpkUIF/Y3wk4Nl3jihipv/uKk3hyYeWj5vjLA/nB8QMRLNHNs5x7rv9bCrLYkkH4Be6Wd EvZ9+3FTfOZ7vkgTO3KEIB2uyIw1taA2X9rx/biG6H4Nf7BaaFL/rvJsUShAgA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1729776753; a=rsa-sha256; cv=none; b=SrN1QhgRUAYwP0a/CTzXdojcwRvvWsTfkb64/K19sPouIszv2Gk/MJOTlmJwb2Vmuryv2o 88ObF/Ars+++3aRoDks87lGG/VjMG6Anf2x/UNqm6Fh+CaAgndZqlrCcq2cyLyQBDVmgug 9Ysv+beGB4AufvaoI+W4qI6UYbh6PTFwcHW1+/cQsyXJZ60pIeDAi0vJPJpVlieQVyk3Dm Yv48iGpGvUGbGLIDDpczUkuqpFpxOR21In4ejMBh2WsAjg1c/k2kF7CO6Z72BfMQQ7Mvm3 J2iGM1Z2sgrimIfPH1KvK5fR8ohUrTUMlhj/VOSCI2rnrd+I0YCC5ShmcKktuA== 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 4XZ6KY19wRzkPS; Thu, 24 Oct 2024 13:32:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 49ODWXAf092766; Thu, 24 Oct 2024 13:32:33 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 49ODWXwL092763; Thu, 24 Oct 2024 13:32:33 GMT (envelope-from git) Date: Thu, 24 Oct 2024 13:32:33 GMT Message-Id: <202410241332.49ODWXwL092763@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: a11fc4771c87 - main - biology/mca-calling: Core tools for mCA event calling 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: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-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: a11fc4771c87c8c76e46fda4e85b0bef9cd8cde8 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a11fc4771c87c8c76e46fda4e85b0bef9cd8cde8 commit a11fc4771c87c8c76e46fda4e85b0bef9cd8cde8 Author: Jason W. Bacon AuthorDate: 2024-10-24 13:32:05 +0000 Commit: Jason W. Bacon CommitDate: 2024-10-24 13:32:05 +0000 biology/mca-calling: Core tools for mCA event calling The mca-calling meta-port provides the core tools needed for performing a typical mCA (Mosaic Chromosomal Alteration) analysis, including conversion of SRA VCF files to a format suitable for haplohseq and MoCha, and haplohseq and MoCha event calling. The GWAS analysis that follows is typically done with R-based tools installed within R. --- biology/Makefile | 1 + biology/mca-calling/Makefile | 27 +++++++++++++++++++++++++++ biology/mca-calling/distinfo | 1 + biology/mca-calling/pkg-descr | 5 +++++ 4 files changed, 34 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 192c77a0d63f..3f12e044804a 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -108,6 +108,7 @@ SUBDIR += mafft SUBDIR += mapm3 SUBDIR += mashmap + SUBDIR += mca-calling SUBDIR += megahit SUBDIR += metaeuk SUBDIR += migrate diff --git a/biology/mca-calling/Makefile b/biology/mca-calling/Makefile new file mode 100644 index 000000000000..5f2afd08795f --- /dev/null +++ b/biology/mca-calling/Makefile @@ -0,0 +1,27 @@ +PORTNAME= mca-calling +DISTVERSION= 0.1.0 +CATEGORIES= biology +MASTER_SITES= # empty + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Core tools for Mosaic Chromosomal Alteration event calling +WWW= https://github.com/auerlab/ + +LICENSE= BSD2CLAUSE + +RUN_DEPENDS+= sra-tools>0:biology/sra-tools +RUN_DEPENDS+= bcftools>0:biology/bcftools +RUN_DEPENDS+= samtools>0:biology/samtools +RUN_DEPENDS+= vcf-split>0:biology/vcf-split +RUN_DEPENDS+= ad2vcf>0:biology/ad2vcf +RUN_DEPENDS+= vcf2hap>0:biology/vcf2hap +RUN_DEPENDS+= haplohseq>0:biology/haplohseq +RUN_DEPENDS+= bio-mocha>0:biology/bio-mocha +RUN_DEPENDS+= bedtools>0:biology/bedtools +RUN_DEPENDS+= mawk>0:lang/mawk +RUN_DEPENDS+= curl>0:ftp/curl +RUN_DEPENDS+= liblz4>0:archivers/liblz4 + +USES= metaport + +.include diff --git a/biology/mca-calling/distinfo b/biology/mca-calling/distinfo new file mode 100644 index 000000000000..d649a5847c66 --- /dev/null +++ b/biology/mca-calling/distinfo @@ -0,0 +1 @@ +TIMESTAMP = 1729776668 diff --git a/biology/mca-calling/pkg-descr b/biology/mca-calling/pkg-descr new file mode 100644 index 000000000000..23486297ac55 --- /dev/null +++ b/biology/mca-calling/pkg-descr @@ -0,0 +1,5 @@ +The mca-calling meta-port provides the core tools needed for performing +a typical mCA (Mosaic Chromosomal Alteration) analysis, including +conversion of SRA VCF files to a format suitable for haplohseq and +MoCha, and haplohseq and MoCha event calling. The GWAS analysis that +follows is typically done with R-based tools installed within R.