Date: Sun, 18 Apr 2021 21:27:59 +0200 From: Mateusz Piotrowski <0mp@FreeBSD.org> To: "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: <5fffb95d-f470-6fe3-936e-7bd34f09e9be@FreeBSD.org> In-Reply-To: <202104181847.13IIl8nX040293@gitrepo.freebsd.org> References: <202104181847.13IIl8nX040293@gitrepo.freebsd.org>
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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=3D5164d38ee538f6791a25b8= 1f28a27126b90444f7 > > commit 5164d38ee538f6791a25b81f28a27126b90444f7 > Author: Jason W. Bacon <jwb@FreeBSD.org> > AuthorDate: 2021-04-18 18:46:14 +0000 > Commit: Jason W. Bacon <jwb@FreeBSD.org> > CommitDate: 2021-04-18 18:46:29 +0000 > > biology/snpeff: Genetic variant annotation and effect prediction t= oolbox [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=3D snpeff > +DISTVERSION=3D 5.0 > +CATEGORIES=3D biology java python > +MASTER_SITES=3D https://snpeff.blob.core.windows.net/versions/ > +DISTNAME=3D 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 ${WRKSRC}/scripts/snpSift A minor style issue: the targets are out of order. > + > +.include <bsd.port.mk> [snip] > --- /dev/null > +++ b/biology/snpeff/files/patch-scripts_snpEff > @@ -0,0 +1,27 @@ > +--- scripts/snpEff.orig 2021-04-13 22:55:13 UTC > ++++ scripts/snpEff > +@@ -13,9 +13,10 @@ > + # Created by: Brad Chapman > + #--------------------------------------------------------------------= ------------------------------- > + > +-jardir=3D"$(cd "$(dirname "$0")" && cd ".." && pwd -P)" > ++jardir=3D%%JAVAJARDIR%%/snpeff > ++userdir=3D~/snpEff > ++JAVA_HOME=3D%%PREFIX%%/openjdk12 This should probably be LOCALBASE instead of PREFIX. Also, it's probably = better to just pass=20 JAVA_HOME to REINPLACE_CMD (as currently this port is going to break if i= t uses a Java version other=20 than OpenJDK 12 (and the Makefile specifies 12+). Cheers, Mateusz
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