Commit 535ff117 authored by Rene Ladan's avatar Rene Ladan
Browse files

biology/snpeff: Remove expired port 

2026-01-31 biology/snpeff: unfetchable
parent e067f9fd

MOVED

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@@ -5100,3 +5100,4 @@ sysutils/burp-devel|sysutils/burp|2026-02-01|Has expired: 3.2.0 is the new stabl 
sysutils/stressdisk||2026-02-01|Has expired: dead upstream

archivers/py-brotlipy|archivers/py-brotlicffi|2026-02-01|Has expired: This project has been archived. The maintainers of this project have marked this project as archived. No new releases are expected. Use archivers/py-brotlicffi instead

x11-fonts/symbola||2026-02-01|Has expired: Unfetchable

biology/snpeff||2026-02-01|Has expired: Unfetchable

biology/Makefile

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@@ -228,7 +228,6 @@ 
    SUBDIR += sigviewer

    SUBDIR += slclust

    SUBDIR += smithwaterman

    SUBDIR += snpeff

    SUBDIR += spoa

    SUBDIR += sra-tools

    SUBDIR += stacks

biology/snpeff/Makefile

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PORTNAME=	snpeff

DISTVERSION=	5.1

CATEGORIES=	biology java python

MASTER_SITES=	https://snpeff.blob.core.windows.net/versions/

DISTNAME=	snpEff_latest_core

DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}



MAINTAINER=	jwb@FreeBSD.org

COMMENT=	Genetic variant annotation and effect prediction toolbox

WWW=		https://snpeff.sourceforge.net/



LICENSE=	MIT

LICENSE_FILE=	${WRKSRC}/LICENSE.md



BROKEN=		Unfetchable

EXPIRATION_DATE=2026-01-31



RUN_DEPENDS=	bash:shells/bash



USES=		java python shebangfix zip



JAVA_VERSION=	17+

SHEBANG_FILES=	scripts/* scripts/gsa/*



NO_BUILD=	yes

NO_ARCH=	yes

WRKSRC=		${WRKDIR}/snpEff



LIBEXEC_DIR=	${PREFIX}/libexec/snpeff



pre-configure:

	${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \

			 -e 's|%%JAVA_HOME%%|${JAVA_HOME}|g' \

			 ${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift



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}



.include <bsd.port.mk>

biology/snpeff/distinfo

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TIMESTAMP = 1671473460

SHA256 (snpeff-5.1/snpEff_latest_core.zip) = 919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b

SIZE (snpeff-5.1/snpEff_latest_core.zip) = 67191760

biology/snpeff/files/patch-scripts_snpEff

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--- scripts/snpEff.orig	2021-04-19 15:55:06 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=%%JAVA_HOME%%

 

-java=java

 if [ -e "$JAVA_HOME/bin/java" ]

 then

 	java="$JAVA_HOME/bin/java"

@@ -43,8 +44,9 @@ if [ "$jvm_mem_opts" == "" ]; then

     jvm_mem_opts="$default_jvm_mem_opts"

 fi

 if [[ "$pass_args" != "" && ! "$pass_args" =~ "-c " ]]; then

-    pass_args="$pass_args -c ${jardir}/snpEff.config"

+    pass_args="$pass_args -c ${userdir}/snpEff.config"

 fi

 

+mkdir -p ~/snpEff

+cp ${jardir}/*.config ~/snpEff

 exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpEff.jar $pass_args

-exit