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

[Mathieu Arnold]

On Sun, Apr 18, 2021 at 09:27:59PM +0200, Mateusz Piotrowski wrote:
> 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.

not may, must.

> > +
> > +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
> 
> 
> 
> 

-- 
Mathieu Arnold
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