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

[Mateusz Piotrowski]

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=5164d38ee538f6791a25b81f28a27126b90444f7
>
> commit 5164d38ee538f6791a25b81f28a27126b90444f7
> Author:     Jason W. Bacon <jwb at FreeBSD.org>
> AuthorDate: 2021-04-18 18:46:14 +0000
> Commit:     Jason W. Bacon <jwb at FreeBSD.org>
> CommitDate: 2021-04-18 18:46:29 +0000
>
>      biology/snpeff: Genetic variant annotation and effect prediction toolbox
[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=	snpeff
> +DISTVERSION=	5.0
> +CATEGORIES=	biology java python
> +MASTER_SITES=	https://snpeff.blob.core.windows.net/versions/
> +DISTNAME=	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 ${WRKSRC}/scripts/snpSift
A minor style issue: the targets are out of order.
> +
> +.include <bsd.port.mk>
[snip]
> --- /dev/null
> +++ b/biology/snpeff/files/patch-scripts_snpEff
> @@ -0,0 +1,27 @@
> +--- scripts/snpEff.orig	2021-04-13 22:55:13 UTC
> ++++ scripts/snpEff
> +@@ -13,9 +13,10 @@
> + # Created by: Brad Chapman
> + #---------------------------------------------------------------------------------------------------
> +
> +-jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)"
> ++jardir=%%JAVAJARDIR%%/snpeff
> ++userdir=~/snpEff
> ++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+).

Cheers,

Mateusz