From owner-dev-commits-ports-main@freebsd.org Sun Apr 18 19:27:52 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 647F65F2619; Sun, 18 Apr 2021 19:27:52 +0000 (UTC) (envelope-from mpp302@gmail.com) Received: from mail-ej1-f44.google.com (mail-ej1-f44.google.com [209.85.218.44]) (using TLSv1.3 with cipher TLS_AES_128_GCM_SHA256 (128/128 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (2048 bits) client-digest SHA256) (Client CN "smtp.gmail.com", Issuer "GTS CA 1O1" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FNg2c1Nqvz4SKX; Sun, 18 Apr 2021 19:27:51 +0000 (UTC) (envelope-from mpp302@gmail.com) Received: by mail-ej1-f44.google.com with SMTP id sd23so40970800ejb.12; Sun, 18 Apr 2021 12:27:51 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:to:references:from:subject:message-id:date :user-agent:mime-version:in-reply-to:content-transfer-encoding :content-language; bh=5PwP/OuXMRZTeaR8yJfQmmqwK2tT6o/sdoPEE7HyLOY=; b=Tjl81dPRIsv/SEDgnf9ict0umoBMT1pf5KWMtucojDTqw4YeuWIrvDgx+aEVrLfLkv Q0+DxmSckjrpAwJFw+P6Xg1TERnGVfH8uSHFehdhSLSfnkcOVyQX0C83a1yqmd84gpef Bf+Tqkhbfw5gwWGDE00BzU2eUZx8/VT5QNNnH3/xa8K6lfBR//2lKJ5pFLcSAjd3iKPL 2MVKh0ABskOdXvg268ZoAQEUAwTnk9N0pTHfMX547hwoBnuPu8SHzSNm/FWezYISaKj9 E2jD+1DkibigJ2ZPsZtWaT1s7Y3U/jLED1WQl6MsJ0B+HQdXubsj8wtSTImoxnHGxtb0 HXrw== X-Gm-Message-State: AOAM530icV0WS2sxXyDM7TIqMEuL01t1CKeXzHj+MCPUkoGjxxVCuamZ wJIPPwnJLsHf1eFOTS6gtHT+MJLc8uYaj9sG X-Google-Smtp-Source: ABdhPJwKacrr1QMlMoKfvOgmJ3yCrajB8ZCSnLJR2pQeQFNjLj0Bm2/jJei/bEgw/lNAkg0Dw9RQZQ== X-Received: by 2002:a17:907:d06:: with SMTP id gn6mr16189373ejc.449.1618774070211; Sun, 18 Apr 2021 12:27:50 -0700 (PDT) Received: from [192.168.0.106] (ip5f5bd493.dynamic.kabel-deutschland.de. [95.91.212.147]) by smtp.gmail.com with ESMTPSA id bw14sm8746415ejb.89.2021.04.18.12.27.49 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sun, 18 Apr 2021 12:27:49 -0700 (PDT) To: "Jason W. Bacon" , ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org References: <202104181847.13IIl8nX040293@gitrepo.freebsd.org> From: Mateusz Piotrowski <0mp@FreeBSD.org> Subject: Re: git: 5164d38ee538 - main - biology/snpeff: Genetic variant annotation and effect prediction toolbox Message-ID: <5fffb95d-f470-6fe3-936e-7bd34f09e9be@FreeBSD.org> Date: Sun, 18 Apr 2021 21:27:59 +0200 User-Agent: Mozilla/5.0 (X11; FreeBSD amd64; rv:78.0) Gecko/20100101 Thunderbird/78.9.1 MIME-Version: 1.0 In-Reply-To: <202104181847.13IIl8nX040293@gitrepo.freebsd.org> Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable Content-Language: en-US X-Rspamd-Queue-Id: 4FNg2c1Nqvz4SKX X-Spamd-Bar: ---- Authentication-Results: mx1.freebsd.org; none X-Spamd-Result: default: False [-4.00 / 15.00]; REPLY(-4.00)[] X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 18 Apr 2021 19:27:52 -0000 Hi! On 18/04/2021 20:47, Jason W. Bacon wrote: > The branch main has been updated by jwb: > > URL: https://cgit.FreeBSD.org/ports/commit/?id=3D5164d38ee538f6791a25b8= 1f28a27126b90444f7 > > commit 5164d38ee538f6791a25b81f28a27126b90444f7 > Author: Jason W. Bacon > AuthorDate: 2021-04-18 18:46:14 +0000 > Commit: Jason W. Bacon > CommitDate: 2021-04-18 18:46:29 +0000 > > biology/snpeff: Genetic variant annotation and effect prediction t= oolbox [snip] > diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile > new file mode 100644 > index 000000000000..3973e9a9a792 > --- /dev/null > +++ b/biology/snpeff/Makefile > @@ -0,0 +1,41 @@ > +PORTNAME=3D snpeff > +DISTVERSION=3D 5.0 > +CATEGORIES=3D biology java python > +MASTER_SITES=3D https://snpeff.blob.core.windows.net/versions/ > +DISTNAME=3D snpEff_latest_core Since DISTNAME is not unique you may consider setting DIST_SUBDIR. > + > +do-install: > + ${MKDIR} ${STAGEDIR}${JAVAJARDIR}/snpeff > + ${MKDIR} ${STAGEDIR}${LIBEXEC_DIR} > + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpEff ${STAGEDIR}${PREFIX}/bin > + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpSift ${STAGEDIR}${PREFIX}/bin > + ${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/snpeff > + ${INSTALL_DATA} ${WRKSRC}/*.config ${STAGEDIR}${JAVAJARDIR}/snpeff > + cd ${WRKSRC}/scripts && ${COPYTREE_BIN} . ${STAGEDIR}${LIBEXEC_DIR} > + > +pre-configure: > + ${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \ > + -e 's|%%PREFIX%%|${PREFIX}|g' \ > + ${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift A minor style issue: the targets are out of order. > + > +.include [snip] > --- /dev/null > +++ b/biology/snpeff/files/patch-scripts_snpEff > @@ -0,0 +1,27 @@ > +--- scripts/snpEff.orig 2021-04-13 22:55:13 UTC > ++++ scripts/snpEff > +@@ -13,9 +13,10 @@ > + # Created by: Brad Chapman > + #--------------------------------------------------------------------= ------------------------------- > + > +-jardir=3D"$(cd "$(dirname "$0")" && cd ".." && pwd -P)" > ++jardir=3D%%JAVAJARDIR%%/snpeff > ++userdir=3D~/snpEff > ++JAVA_HOME=3D%%PREFIX%%/openjdk12 This should probably be LOCALBASE instead of PREFIX. Also, it's probably = better to just pass=20 JAVA_HOME to REINPLACE_CMD (as currently this port is going to break if i= t uses a Java version other=20 than OpenJDK 12 (and the Makefile specifies 12+). Cheers, Mateusz