From owner-dev-commits-ports-all@freebsd.org Mon Apr 19 16:12:15 2021 Return-Path: Delivered-To: dev-commits-ports-all@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 A510C5F78AE; Mon, 19 Apr 2021 16:12:15 +0000 (UTC) (envelope-from bacon4000@gmail.com) Received: from mail-qt1-x836.google.com (mail-qt1-x836.google.com [IPv6:2607:f8b0:4864:20::836]) (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 4FPBfR42BTz4b7N; Mon, 19 Apr 2021 16:12:15 +0000 (UTC) (envelope-from bacon4000@gmail.com) Received: by mail-qt1-x836.google.com with SMTP id u8so26419247qtq.12; Mon, 19 Apr 2021 09:12:15 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:cc:references:from:message-id:date:user-agent :mime-version:in-reply-to:content-transfer-encoding:content-language; bh=dEgH3kwgnvi/3qPFiiehlMJxY0lo4cqGsWXqGLLmDeU=; b=Dbu5VPxhm91BT7foCPfeMqAvWdO+CNJ0vy1C3FDdpVzmtLP7enenF9GL6SLHubO4Oj +6Y5P0xlZXxRNCSaXn4+vbjVxwgTTQvHvWQteTFOtSVGhyZILnE8gbVqBuak0gnD6Yu9 3+0P3Bdfp1G3HAh3SDxt/5Sf9gqUn9cTkKaiC7mUs/Tiz2oWynFAAdWEqkyNAfj2FfO/ DPj3pEB8rUoaW68I5tosNHgs2OZDsRi1UB83s6m0W+GawsGnfaCZbrnU2WY70bTpfI+p EkAQxmlyIsZCcyJeCi4QPqiDuP9oa33O55doM1nlfC4xBjFV2Js1fKWdnbE1geyeyZiW qMKA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:cc:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-transfer-encoding :content-language; bh=dEgH3kwgnvi/3qPFiiehlMJxY0lo4cqGsWXqGLLmDeU=; b=dE/QyBZLLs9T2EEFqM91YOFVCZYxGj6oo5YJE17J9z1VFctNwdpPykJ5EgetPw4Cpa 6jcjw/lh0Q5Tdua60mDIQepnmoanfANEsXlsGF0j2QAhtD4F0le8ReNBbzPd5D15QEfg FfGt5ikP4Xi+yeEyk0wlKw4Vrt3CJS/sn6UfVH8ZU7SMxU0vu4FLM6MOHnFMeoE6/MiL xK9JbUZ+MgiWNCdYV/JvC67oxD+FwFCWHK5TMi8NNU2u/VgPlxtsN1m048NmpEPXOXTk 4U6w3abKXOxOfk26SesoJfmhR8/Vvc//Ue1R5XOE0wvwmwieRaxZdwKpDtqansPMFI+3 UmFA== X-Gm-Message-State: AOAM533DFwT0O6FYknnSXSYaQHfO3jU/EZV7mdnk1y4Ek/rz+8yLBLhC +SWUmAv2tcs6MMi9KJPLCloFtkstMLw= X-Google-Smtp-Source: ABdhPJy7ciNQa6Hkhv48ISs16OiCZHYYuRD9EDbpQjck+ijzh22bfinWvstgx/QBiG/G16WMwF+8nw== X-Received: by 2002:ac8:7dd2:: with SMTP id c18mr12481084qte.301.1618848734356; Mon, 19 Apr 2021 09:12:14 -0700 (PDT) Received: from coral.acadix.biz (2603-6000-a401-3a00-0223-24ff-fe37-c4d7.res6.spectrum.com. [2603:6000:a401:3a00:223:24ff:fe37:c4d7]) by smtp.gmail.com with ESMTPSA id n15sm9905557qkk.109.2021.04.19.09.12.13 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Mon, 19 Apr 2021 09:12:13 -0700 (PDT) Subject: Re: git: 5164d38ee538 - main - biology/snpeff: Genetic variant annotation and effect prediction toolbox To: Mathieu Arnold , Mateusz Piotrowski <0mp@freebsd.org> Cc: "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> <5fffb95d-f470-6fe3-936e-7bd34f09e9be@FreeBSD.org> <20210419090342.bc5hep4f3wyggql6@aching.in.mat.cc> From: Jason Bacon Message-ID: <9839d650-cabc-1ad1-0f5b-fabecd3fb9d1@gmail.com> Date: Mon, 19 Apr 2021 11:12:12 -0500 User-Agent: Mozilla/5.0 (X11; FreeBSD amd64; rv:78.0) Gecko/20100101 Thunderbird/78.9.1 MIME-Version: 1.0 In-Reply-To: <20210419090342.bc5hep4f3wyggql6@aching.in.mat.cc> Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: quoted-printable Content-Language: en-US X-Rspamd-Queue-Id: 4FPBfR42BTz4b7N 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-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Apr 2021 16:12:15 -0000 On 4/19/21 4:03 AM, Mathieu Arnold wrote: > On Sun, Apr 18, 2021 at 09:27:59PM +0200, Mateusz Piotrowski wrote: >> Hi! >> >> Since DISTNAME is not unique you may consider setting DIST_SUBDIR. > not may, must. Yeah, I should have caught that one, thanks! >>> + >>> +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}/bi= n >>> + ${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. That's just fatigue...=A0 ;-/ >> >>> ++JAVA_HOME=3D%%PREFIX%%/openjdk12 >> This should probably be LOCALBASE instead of PREFIX. Also, it's probab= ly >> better to just pass JAVA_HOME to REINPLACE_CMD (as currently this port=20 is >> going to break if it uses a Java version other than OpenJDK 12 (and th= e >> Makefile specifies 12+). Good idea! Best, =A0=A0=A0 JB --=20 Earth is a beta site.