git: bd40198f6b3d - main - biology/artemis: update 17.0.1-11 → 18.2.0

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 18 Oct 2026 17:22:40 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=bd40198f6b3d49d2a80e5b2be2359e4210a73f62

commit bd40198f6b3d49d2a80e5b2be2359e4210a73f62
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-10-18 16:15:00 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-10-18 17:22:35 +0000

    biology/artemis: update 17.0.1-11 → 18.2.0
---
 biology/artemis/Makefile  | 66 ++++++++++++++++++++++++++++--------
 biology/artemis/distinfo  |  8 +++--
 biology/artemis/pkg-plist | 85 +++--------------------------------------------
 3 files changed, 62 insertions(+), 97 deletions(-)

diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile
index 5cc68cfac884..0c36713d8a5b 100644
--- a/biology/artemis/Makefile
+++ b/biology/artemis/Makefile
@@ -1,42 +1,80 @@
 PORTNAME=	artemis
 DISTVERSIONPREFIX=	v
-DISTVERSION=	17.0.1-11
-PORTREVISION=	2
-DISTVERSIONSUFFIX=	-g3e43d27e
+DISTVERSION=	18.2.0
 CATEGORIES=	biology java
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	DNA sequence viewer and annotation tool
-WWW=		https://www.sanger.ac.uk/science/tools/artemis
+WWW=		https://www.sanger.ac.uk/tool/artemis/ \
+		https://github.com/sanger-pathogens/Artemis
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+BUILD_DEPENDS=	maven310>0:devel/maven310
 RUN_DEPENDS=	bash:shells/bash
 
-USES=		gmake java shebangfix
+USES=		java shebangfix
 USE_GITHUB=	yes
 GH_ACCOUNT=	sanger-pathogens
 SHEBANG_FILES=	act art bamview dnaplotter test/*.sh etc/go_associations.pl
-ALL_TARGET=	jar
 NO_ARCH=	yes
 
+MAKE_ENV+=	JAVA_HOME=${JAVA_HOME}
+
 PLIST_SUB=	PORTVERSION="${PORTVERSION}"
 
+# to rebuild the deps archive:
+#   1. set DEV_UPDATE_MODE=yes
+#   2. make makesum build
+#   3. upload the *-deps archive
+#   4. set DEV_UPDATE_MODE=no
+#   5. make clean makesum
+
+DEV_UPDATE_MODE=	no
+
+.if (${DEV_UPDATE_MODE} != "yes")
+MASTER_SITES+=	LOCAL/yuri/:deps
+DISTFILES+=	${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
+MVN_ARGS=	--offline
+.endif
+
 post-extract:
-	@cd ${WRKDIR} && ${MV} Artemis-${DISTVERSION}${DISTVERSIONSUFFIX} ${PORTNAME}-${DISTVERSION}${DISTVERSIONSUFFIX}
+	@cd ${WRKDIR} && ${MV} Artemis-${DISTVERSION} ${PORTNAME}-${DISTVERSION}
 
-do-install:
-	@${MKDIR} ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}
-.for f in jar_build lib etc images artemis_sqlmap
-	@cd ${WRKSRC} && ${COPYTREE_SHARE} ${f} ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}
+do-build: # validate installs the bundled legacy jars into the local repository and must run in a separate invocation
+.for t in validate package
+	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
+		${LOCALBASE}/bin/mvn ${MVN_ARGS} \
+		-Dmaven.test.skip=true \
+		-Duser.home=${WRKDIR} \
+		${t}
 .endfor
-	@cd ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION} && ${MV} jar_build jars
+
+.if (${DEV_UPDATE_MODE} == "yes")
+post-build: do-test
+	@cd ${WRKDIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} .m2
+	@${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
+.endif
+
+# tests excluded below need network access, a display or EMBOSS
+do-test:
+	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
+		${LOCALBASE}/bin/mvn ${MVN_ARGS} \
+		-Duser.home=${WRKDIR} \
+		-Dtest='!BamUtilsTest,!CircularGenomeControllerTest,!RunBlastAtNCBITest,!TestIbatisDAO,!TestJdbcDAO,!WriteVCFTest,!WriteVariantSitesTest' \
+		test
+
+do-install:
+	@${MKDIR} ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}/target
+	@cd ${WRKSRC} && ${COPYTREE_SHARE} etc ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}
+	@cd ${WRKSRC}/target && ${COPYTREE_SHARE} jars ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}/target
 .for f in art act bamview dnaplotter
 	${INSTALL_SCRIPT} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}/${f}
-	@${REINPLACE_CMD} -i '' -e 's|APPLICATION_HOME=.*|&/jars|' ${STAGEDIR}${PREFIX}/${PORTNAME}-${PORTVERSION}/${f}
-	@(${ECHO} "#!/bin/sh"; ${ECHO} ""; ${ECHO} "cd ${PREFIX}/${PORTNAME}-${PORTVERSION} && ./${f}") > ${STAGEDIR}${PREFIX}/bin/${f}
+	@(${ECHO} "#!/bin/sh"; ${ECHO} ""; ${ECHO} "cd ${PREFIX}/${PORTNAME}-${PORTVERSION} && ./${f} \""$$"@\"") > ${STAGEDIR}${PREFIX}/bin/${f}
 	@${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${f}
 .endfor
 
+# tests as of 18.2.0: Tests run: 281, Failures: 0, Errors: 0, Skipped: 1
+
 .include <bsd.port.mk>
diff --git a/biology/artemis/distinfo b/biology/artemis/distinfo
index 5bfcefd6de95..88e08f2a7b52 100644
--- a/biology/artemis/distinfo
+++ b/biology/artemis/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1528734532
-SHA256 (sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz) = a490d4b76bfdd8a531d22f2e0495e8c2c6e8efad18e6a9a0043ac425c7ab16dc
-SIZE (sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz) = 77195529
+TIMESTAMP = 1792339000
+SHA256 (artemis-18.2.0-deps.tar.gz) = 37e047b35d905ddbc6b8af1f3daa0971d4e4e029ee78341bc4608317d9ed4c85
+SIZE (artemis-18.2.0-deps.tar.gz) = 80223690
+SHA256 (sanger-pathogens-artemis-v18.2.0_GH0.tar.gz) = 842c055f5cce021adbaea4f076b2ea80335ab1e44fbaa34b2ab608df6314a18e
+SIZE (sanger-pathogens-artemis-v18.2.0_GH0.tar.gz) = 18847117
diff --git a/biology/artemis/pkg-plist b/biology/artemis/pkg-plist
index de896ef0b5e6..fcff26cb622c 100644
--- a/biology/artemis/pkg-plist
+++ b/biology/artemis/pkg-plist
@@ -1,30 +1,5 @@
 artemis-%%PORTVERSION%%/act
 artemis-%%PORTVERSION%%/art
-artemis-%%PORTVERSION%%/artemis_sqlmap/Analysis.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/AnalysisFeature.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/Cv.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/CvTerm.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/Db.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/DbXRef.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/Feature.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTerm.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTermDbXRef.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTermProp.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureCvTermPub.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureDbXRef.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureLoc.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureProp.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeaturePub.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureRelationship.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/FeatureSynonym.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/Graph.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/Organism.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/OrganismProp.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/Pub.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/PubDbXRef.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/Synonym.xml
-artemis-%%PORTVERSION%%/artemis_sqlmap/chado_iBatis_config.properties
-artemis-%%PORTVERSION%%/artemis_sqlmap/chado_iBatis_config.xml
 artemis-%%PORTVERSION%%/bamview
 artemis-%%PORTVERSION%%/dnaplotter
 artemis-%%PORTVERSION%%/etc/af063097.embl
@@ -43,7 +18,6 @@ artemis-%%PORTVERSION%%/etc/feature_keys_gff
 artemis-%%PORTVERSION%%/etc/go_associations.pl
 artemis-%%PORTVERSION%%/etc/key_mapping
 artemis-%%PORTVERSION%%/etc/log4j.properties
-artemis-%%PORTVERSION%%/etc/log4j.properties.txt
 artemis-%%PORTVERSION%%/etc/options
 artemis-%%PORTVERSION%%/etc/pombe.usage
 artemis-%%PORTVERSION%%/etc/project.properties
@@ -53,71 +27,22 @@ artemis-%%PORTVERSION%%/etc/qualifier_types_gff
 artemis-%%PORTVERSION%%/etc/readmeDNADraw.html
 artemis-%%PORTVERSION%%/etc/results_to_netscape
 artemis-%%PORTVERSION%%/etc/run_blastn
-artemis-%%PORTVERSION%%/etc/run_blastn.sanger
 artemis-%%PORTVERSION%%/etc/run_blastp
-artemis-%%PORTVERSION%%/etc/run_blastp.sanger
-artemis-%%PORTVERSION%%/etc/run_blastp.sanger.linux
 artemis-%%PORTVERSION%%/etc/run_blastx
-artemis-%%PORTVERSION%%/etc/run_blastx.sanger
 artemis-%%PORTVERSION%%/etc/run_clustalx
-artemis-%%PORTVERSION%%/etc/run_clustalx.sanger
-artemis-%%PORTVERSION%%/etc/run_fasta
-artemis-%%PORTVERSION%%/etc/run_fasta.sanger
-artemis-%%PORTVERSION%%/etc/run_fasta.sanger.linux
-artemis-%%PORTVERSION%%/etc/run_fastx
-artemis-%%PORTVERSION%%/etc/run_fastx.sanger
 artemis-%%PORTVERSION%%/etc/run_hth
-artemis-%%PORTVERSION%%/etc/run_jalview
 artemis-%%PORTVERSION%%/etc/run_netblastp
 artemis-%%PORTVERSION%%/etc/run_pepstats
 artemis-%%PORTVERSION%%/etc/run_sigcleave
-artemis-%%PORTVERSION%%/etc/run_smart
 artemis-%%PORTVERSION%%/etc/run_tblastn
 artemis-%%PORTVERSION%%/etc/run_tblastx
-artemis-%%PORTVERSION%%/etc/run_tblastx.sanger
+artemis-%%PORTVERSION%%/etc/setup_blast_dbs.sh
 artemis-%%PORTVERSION%%/etc/versions
 artemis-%%PORTVERSION%%/etc/writedb_entry
-artemis-%%PORTVERSION%%/images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg
-artemis-%%PORTVERSION%%/images/act.gif
-artemis-%%PORTVERSION%%/images/helix.gif
-artemis-%%PORTVERSION%%/images/icon.gif
-artemis-%%PORTVERSION%%/images/sanger-centre.gif
-artemis-%%PORTVERSION%%/jars/act.jar
-artemis-%%PORTVERSION%%/jars/artemis.jar
-artemis-%%PORTVERSION%%/jars/bamview.jar
-artemis-%%PORTVERSION%%/jars/dnaplotter.jar
-artemis-%%PORTVERSION%%/lib/LICENSE.Apache
-artemis-%%PORTVERSION%%/lib/LICENSE.JDBC
-artemis-%%PORTVERSION%%/lib/LICENSE.Picard
-artemis-%%PORTVERSION%%/lib/README
-artemis-%%PORTVERSION%%/lib/batik/batik-awt-util.jar
-artemis-%%PORTVERSION%%/lib/batik/batik-codec.jar
-artemis-%%PORTVERSION%%/lib/batik/batik-dom.jar
-artemis-%%PORTVERSION%%/lib/batik/batik-ext.jar
-artemis-%%PORTVERSION%%/lib/batik/batik-svggen.jar
-artemis-%%PORTVERSION%%/lib/batik/batik-util.jar
-artemis-%%PORTVERSION%%/lib/batik/batik-xml.jar
-artemis-%%PORTVERSION%%/lib/batik/version
-artemis-%%PORTVERSION%%/lib/biojava.jar
-artemis-%%PORTVERSION%%/lib/commons-lang-2.6.jar
-artemis-%%PORTVERSION%%/lib/commons-net-3.6.jar
-artemis-%%PORTVERSION%%/lib/ibatis/README
-artemis-%%PORTVERSION%%/lib/ibatis/cglib-nodep-2.2.jar
-artemis-%%PORTVERSION%%/lib/ibatis/ibatis-2.3.4.726.jar
-artemis-%%PORTVERSION%%/lib/ibatis/license.txt
-artemis-%%PORTVERSION%%/lib/ibatis/log4j-1.2.14.jar
-artemis-%%PORTVERSION%%/lib/j2ssh/COMMONS.LICENSE
-artemis-%%PORTVERSION%%/lib/j2ssh/J2SSH.LICENSE
-artemis-%%PORTVERSION%%/lib/j2ssh/README
-artemis-%%PORTVERSION%%/lib/j2ssh/commons-logging.jar
-artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh-artemis-plugin.jar
-artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh-core.jar
-artemis-%%PORTVERSION%%/lib/j2ssh/j2ssh.properties
-artemis-%%PORTVERSION%%/lib/jakarta-regexp-1.2.jar
-artemis-%%PORTVERSION%%/lib/jemAlign.jar
-artemis-%%PORTVERSION%%/lib/picard/VERSION.txt
-artemis-%%PORTVERSION%%/lib/picard/picard.jar
-artemis-%%PORTVERSION%%/lib/postgresql-8.4-701.jdbc3.jar
+artemis-%%PORTVERSION%%/target/jars/act.jar
+artemis-%%PORTVERSION%%/target/jars/artemis.jar
+artemis-%%PORTVERSION%%/target/jars/bamview.jar
+artemis-%%PORTVERSION%%/target/jars/dnaplotter.jar
 bin/act
 bin/art
 bin/bamview