git: 535ff1176ab7 - main - biology/snpeff: Remove expired port

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From: Rene Ladan <rene_at_FreeBSD.org>
Date: Sun, 01 Feb 2026 10:54:16 UTC
The branch main has been updated by rene:

URL: https://cgit.FreeBSD.org/ports/commit/?id=535ff1176ab778305597c3d773eb8b43558812ce

commit 535ff1176ab778305597c3d773eb8b43558812ce
Author:     Rene Ladan <rene@FreeBSD.org>
AuthorDate: 2026-02-01 10:54:01 +0000
Commit:     Rene Ladan <rene@FreeBSD.org>
CommitDate: 2026-02-01 10:54:04 +0000

    biology/snpeff: Remove expired port
    
    2026-01-31 biology/snpeff: unfetchable
---
 MOVED                                      |  1 +
 biology/Makefile                           |  1 -
 biology/snpeff/Makefile                    | 45 ------------------
 biology/snpeff/distinfo                    |  3 --
 biology/snpeff/files/patch-scripts_snpEff  | 27 -----------
 biology/snpeff/files/patch-scripts_snpSift | 19 --------
 biology/snpeff/pkg-descr                   | 12 -----
 biology/snpeff/pkg-plist                   | 75 ------------------------------
 8 files changed, 1 insertion(+), 182 deletions(-)

diff --git a/MOVED b/MOVED
index a4171a8128df..f1cdabf71627 100644
--- a/MOVED
+++ b/MOVED
@@ -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 archivers/py-brotlipy|archivers/py-brotlicffi|2026-02-01|Has expired: This project has been archived.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
diff --git a/biology/Makefile b/biology/Makefile
index d4ba88800bfe..bad75e81fbd1 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -228,7 +228,6 @@
     SUBDIR += sigviewer
     SUBDIR += slclust
     SUBDIR += smithwaterman
-    SUBDIR += snpeff
     SUBDIR += spoa
     SUBDIR += sra-tools
     SUBDIR += stacks
diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile
deleted file mode 100644
index 1d3e325a7e11..000000000000
--- a/biology/snpeff/Makefile
+++ /dev/null
@@ -1,45 +0,0 @@
-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>
diff --git a/biology/snpeff/distinfo b/biology/snpeff/distinfo
deleted file mode 100644
index f57ab2e7febf..000000000000
--- a/biology/snpeff/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-TIMESTAMP = 1671473460
-SHA256 (snpeff-5.1/snpEff_latest_core.zip) = 919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b
-SIZE (snpeff-5.1/snpEff_latest_core.zip) = 67191760
diff --git a/biology/snpeff/files/patch-scripts_snpEff b/biology/snpeff/files/patch-scripts_snpEff
deleted file mode 100644
index d15b83ad84e0..000000000000
--- a/biology/snpeff/files/patch-scripts_snpEff
+++ /dev/null
@@ -1,27 +0,0 @@
---- 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 $pass_args
--exit
diff --git a/biology/snpeff/files/patch-scripts_snpSift b/biology/snpeff/files/patch-scripts_snpSift
deleted file mode 100644
index c76fa3c4fcfd..000000000000
--- a/biology/snpeff/files/patch-scripts_snpSift
+++ /dev/null
@@ -1,19 +0,0 @@
---- scripts/snpSift.orig	2021-04-19 15:55:06 UTC
-+++ scripts/snpSift
-@@ -13,9 +13,9 @@
- # Created by: Brad Chapman
- #---------------------------------------------------------------------------------------------------
- 
--jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)"
-+jardir=%%JAVAJARDIR%%/snpeff
-+JAVA_HOME=%%JAVA_HOME%%
- 
--java=java
- if [ -e "$JAVA_HOME/bin/java" ]
- then
- 	java="$JAVA_HOME/bin/java"
-@@ -44,4 +44,3 @@ if [ "$jvm_mem_opts" == "" ]; then
- fi
- 
- exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/SnpSift.jar $pass_args
--exit
diff --git a/biology/snpeff/pkg-descr b/biology/snpeff/pkg-descr
deleted file mode 100644
index 2d4fca4d95da..000000000000
--- a/biology/snpeff/pkg-descr
+++ /dev/null
@@ -1,12 +0,0 @@
-Genetic variant annotation and functional effect prediction toolbox. It
-annotates and predicts the effects of genetic variants on genes and proteins
-(such as amino acid changes).
-
-Features:
-
-    Supports over 38,000 genomes
-    Standard ANN annotation format
-    Cancer variants analysis
-    GATK compatible (-o gatk)
-    HGVS notation
-    Sequence Ontology standardized terms
diff --git a/biology/snpeff/pkg-plist b/biology/snpeff/pkg-plist
deleted file mode 100644
index a004332b0b41..000000000000
--- a/biology/snpeff/pkg-plist
+++ /dev/null
@@ -1,75 +0,0 @@
-bin/snpEff
-bin/snpSift
-libexec/snpeff/1kg.sh
-libexec/snpeff/annotate_demo.sh
-libexec/snpeff/annotate_demo_GATK.sh
-libexec/snpeff/bedEffOnePerLine.pl
-libexec/snpeff/buildDbNcbi.sh
-libexec/snpeff/cgShore.pl
-libexec/snpeff/cgShore.sh
-libexec/snpeff/countColumns.py
-libexec/snpeff/db.pl
-libexec/snpeff/extractSequences.pl
-libexec/snpeff/fasta2tab.pl
-libexec/snpeff/fastaSample.pl
-libexec/snpeff/fastaSplit.pl
-libexec/snpeff/fastqSplit.pl
-libexec/snpeff/filterBy.py
-libexec/snpeff/gffRemovePhase.pl
-libexec/snpeff/gsa/bayesFactor_correction_scoreCount.r
-libexec/snpeff/gsa/bayesFactor_correction_scoreCount.sh
-libexec/snpeff/gsa/bayesFactor_correction_scoreCount_max10.sh
-libexec/snpeff/gsa/checkGeneNames.py
-libexec/snpeff/gsa/create_sets.bds
-libexec/snpeff/gsa/geneSetOverlap.py
-libexec/snpeff/gsa/geneSetOverlap.sort.txt
-libexec/snpeff/gsa/geneSetsGtex.py
-libexec/snpeff/gsa/pvalue_correction_scoreCount.r
-libexec/snpeff/gsa/pvalue_correction_scoreCount.sh
-libexec/snpeff/gsa/pvalue_correction_scoreCount_min10.sh
-libexec/snpeff/isutf8.py
-libexec/snpeff/join.pl
-libexec/snpeff/joinSnpEff.pl
-libexec/snpeff/make_and_commit_docs.sh
-libexec/snpeff/make_dbNSFP.sh
-libexec/snpeff/nextProt_filter.pl
-libexec/snpeff/ped2vcf.py
-libexec/snpeff/plot.pl
-libexec/snpeff/plotHistogram.pl
-libexec/snpeff/plotLabel.pl
-libexec/snpeff/plotMA.pl
-libexec/snpeff/plotQQ.pl
-libexec/snpeff/plotQQsubsample.pl
-libexec/snpeff/plotSmoothScatter.pl
-libexec/snpeff/plotXY.pl
-libexec/snpeff/queue.pl
-libexec/snpeff/sam2fastq.pl
-libexec/snpeff/sample.pl
-libexec/snpeff/snpEff
-libexec/snpeff/snpEff.bak
-libexec/snpeff/snpEff.orig
-libexec/snpeff/snpSift
-libexec/snpeff/snpSift.orig
-libexec/snpeff/snpSift_filter_sample_to_number.pl
-libexec/snpeff/sortLine.py
-libexec/snpeff/splitChr.pl
-libexec/snpeff/statsNum.pl
-libexec/snpeff/swapCols.pl
-libexec/snpeff/transpose.pl
-libexec/snpeff/txt2fa.pl
-libexec/snpeff/txt2vcf.py
-libexec/snpeff/uniqCount.pl
-libexec/snpeff/uniqCut.pl
-libexec/snpeff/vcfAnnFirst.py
-libexec/snpeff/vcfBareBones.pl
-libexec/snpeff/vcfEffHighest.ORI.py
-libexec/snpeff/vcfEffOnePerLine.pl
-libexec/snpeff/vcfFilterSamples.pl
-libexec/snpeff/vcfInfoOnePerLine.pl
-libexec/snpeff/vcfOnlyAlts.pl
-libexec/snpeff/vcfReduceGenotypes.pl
-libexec/snpeff/vcfRefCorrect.py
-libexec/snpeff/wigSplit.pl
-%%JAVAJARDIR%%/snpeff/SnpSift.jar
-%%JAVAJARDIR%%/snpeff/snpEff.config
-%%JAVAJARDIR%%/snpeff/snpEff.jar