From nobody Mon Dec 12 17:17:24 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 4NW7bn0L2Mz4kq5S; Mon, 12 Dec 2022 17:17:25 +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 4NW7bm6nWPz3hLM; Mon, 12 Dec 2022 17:17:24 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1670865445; 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=rceAKY3gPBahk9nE/9XJhU5S0jXorGDPv72aw1DypsI=; b=kLd0C7QHDX/a3edd6kEcjBlzphQNjgi2/IQiSXOK1Bs4AJv59vuzum9SdONkihYb43ZHZv upqm357jo/T4yjNwz54r4llsoLLW+on66f47gtbmbRaKymSzgoXegP8WrNSVoCRuj+5sbL z53++6iSXeB0pnmS6w44BJqY5TUlEhlBZWBkOBdWojgf0wP6hs3fXAcMncgK6EJa7G0iJM BjOJk38GzGfb32Up1QcM7IIKNz098TPSCRyUAaQ6BFB82VcLuLO22AXgvBpkXgu87NRcwa 22sPYBuIUGMZpti9xG+hUl8xxAZUJz3fc4lP/D0m6XF/gafeEMJb4gyU+kM3cA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1670865445; 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=rceAKY3gPBahk9nE/9XJhU5S0jXorGDPv72aw1DypsI=; b=HL+hpudaSxbBzx5bW965yZIT3I+gVMZV2dOeGhHOKHbaiW6n5EiVJSYyLZ66mUUQLK6aTb 7Ns45BIEtgRn8ENnvBFKLoAQa7qk/KrEvl2mdjZPRTz3z5+WC8cFEzw9/UInICgd1MDkfq r/Y53e6rSZuVnB8XscezJiybw4r8hegJTZEV9fXq+iY968h/hlSXJEC1tD22RGyORF8aWv M0bbApGMrrLMQEJd5Z1nNbjEv1CMU4FcAfTCdty2FUJLfM0Szyh4TTNSKkWVC4NZqg0Q/r 03KAikN79XE2iWy3CwEVhPQgsMhNaqAgU/HxWE++r91OoVOmgnyxr0D1+Ii17w== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1670865445; a=rsa-sha256; cv=none; b=Wbofn/mWT2hd4iTELxr2J7RmmyPhyLW003US3mhGrvD+rSXrRbIqDfDYFDPqumOID83uE7 C4VKg5Xx79kqQ1FPekVpu202h8nlruRAY7PjJ2Bf5xZ3k9wVMHOOpCWOk9Pzg+9h8ooFe+ oAb8DWTbO7KBybeI42jpqp7JBJQOkXS/IAN4/fEhNiKbdVJ9sf3PZL+s8a689tfcXTjqjm ARce2vbNFW2jk7lwLqQ8SguhDA+0p847YMJegtSBgjxKY0/4EX321Mo1XxKI8uV/t0X0o+ i2Rmir2E3zjZglyjkGJmArnx9+PfF4aN0iGBdlQeAcs13lVK0iTyvCYOEiV6dw== 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 4NW7bm5cpqzhR9; Mon, 12 Dec 2022 17:17:24 +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 2BCHHOin001364; Mon, 12 Dec 2022 17:17:24 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 2BCHHO3A001363; Mon, 12 Dec 2022 17:17:24 GMT (envelope-from git) Date: Mon, 12 Dec 2022 17:17:24 GMT Message-Id: <202212121717.2BCHHO3A001363@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: 455ea913be3f - main - biology/fasda: Fast and simple differential analysis 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: 455ea913be3f86da7096e18368b4ac62e319dbe5 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=455ea913be3f86da7096e18368b4ac62e319dbe5 commit 455ea913be3f86da7096e18368b4ac62e319dbe5 Author: Jason W. Bacon AuthorDate: 2022-12-12 17:17:02 +0000 Commit: Jason W. Bacon CommitDate: 2022-12-12 17:17:22 +0000 biology/fasda: Fast and simple differential analysis FASDA aims to provide a fast and simple differential analysis tool that just works and does not require any knowledge beyond basic Unix command-line skills. The code is written entirely in C to maximize efficiency and portability, and to provide a simple command-line user interface. --- biology/Makefile | 1 + biology/fasda/Makefile | 25 +++++++++++++++++++++++++ biology/fasda/distinfo | 3 +++ biology/fasda/pkg-descr | 5 +++++ biology/fasda/pkg-plist | 10 ++++++++++ 5 files changed, 44 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 0622b83369d4..b544cbf16e59 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -41,6 +41,7 @@ SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate + SUBDIR += fasda SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack diff --git a/biology/fasda/Makefile b/biology/fasda/Makefile new file mode 100644 index 000000000000..eeca4cc01c9f --- /dev/null +++ b/biology/fasda/Makefile @@ -0,0 +1,25 @@ +PORTNAME= fasda +DISTVERSION= 0.1.2 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Fast and simple differential analysis +WWW= https://github.com/auerlab/fasda + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libxtend.so:devel/libxtend libbiolibc.so:biology/biolibc + +USES= localbase +USE_GITHUB= yes + +GH_ACCOUNT= auerlab + +MAKE_ENV= VERSION=${PORTVERSION} +INSTALL_TARGET= install-strip + +pre-build: + cd ${WRKSRC} && make depend LOCALBASE=${LOCALBASE} + +.include diff --git a/biology/fasda/distinfo b/biology/fasda/distinfo new file mode 100644 index 000000000000..c0cdeca0ea7c --- /dev/null +++ b/biology/fasda/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1670865129 +SHA256 (auerlab-fasda-0.1.2_GH0.tar.gz) = ea6003795b462286d4b7ea11924f424cdea418a345ceeccd1a04d679edf2374e +SIZE (auerlab-fasda-0.1.2_GH0.tar.gz) = 57295 diff --git a/biology/fasda/pkg-descr b/biology/fasda/pkg-descr new file mode 100644 index 000000000000..7a5c92fa13d8 --- /dev/null +++ b/biology/fasda/pkg-descr @@ -0,0 +1,5 @@ +FASDA aims to provide a fast and simple differential analysis tool +that just works and does not require any knowledge beyond basic Unix +command-line skills. The code is written entirely in C to maximize +efficiency and portability, and to provide a simple command-line user +interface. diff --git a/biology/fasda/pkg-plist b/biology/fasda/pkg-plist new file mode 100644 index 000000000000..939aed76df22 --- /dev/null +++ b/biology/fasda/pkg-plist @@ -0,0 +1,10 @@ +bin/fasda +libexec/fasda/abundance +libexec/fasda/fold-change +libexec/fasda/normalize +libexec/fasda/pval-sim +man/man1/fasda-abundance.1.gz +man/man1/fasda-fold-change.1.gz +man/man1/fasda-normalize.1.gz +man/man1/fasda-pval-sim.1.gz +man/man1/fasda.1.gz