git: 5164d38ee538 - main - biology/snpeff: Genetic variant annotation and effect prediction toolbox

[Jason Bacon]

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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