Date: Mon, 19 Apr 2021 11:12:12 -0500 From: Jason Bacon <bacon4000@gmail.com> To: Mathieu Arnold <mat@freebsd.org>, Mateusz Piotrowski <0mp@freebsd.org> Cc: "Jason W. Bacon" <jwb@freebsd.org>, ports-committers@freebsd.org, dev-commits-ports-all@freebsd.org, dev-commits-ports-main@freebsd.org Subject: Re: git: 5164d38ee538 - main - biology/snpeff: Genetic variant annotation and effect prediction toolbox Message-ID: <9839d650-cabc-1ad1-0f5b-fabecd3fb9d1@gmail.com> In-Reply-To: <20210419090342.bc5hep4f3wyggql6@aching.in.mat.cc> References: <202104181847.13IIl8nX040293@gitrepo.freebsd.org> <5fffb95d-f470-6fe3-936e-7bd34f09e9be@FreeBSD.org> <20210419090342.bc5hep4f3wyggql6@aching.in.mat.cc>
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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}/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.
That's just fatigue... ;-/
>>
>>> ++JAVA_HOME=%%PREFIX%%/openjdk12
>> This should probably be LOCALBASE instead of PREFIX. Also, it's probably
>> better to just pass JAVA_HOME to REINPLACE_CMD (as currently this port
is
>> going to break if it uses a Java version other than OpenJDK 12 (and the
>> Makefile specifies 12+).
Good idea!
Best,
JB
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