Date: Fri, 9 Jul 2021 12:29:14 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: e44f917e298a - main - biology/erminej: Analyses of gene sets, e.g. gene expression profiling Message-ID: <202107091229.169CTEIj083784@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=e44f917e298a1f860fab0790aacd348cae60f74b commit e44f917e298a1f860fab0790aacd348cae60f74b Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-07-09 12:26:58 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-07-09 12:26:58 +0000 biology/erminej: Analyses of gene sets, e.g. gene expression profiling ErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing something interesting" in an experiment that generates long lists of candidates. The software is designed to be used by biologists with little or no informatics background (but if you do, you might be interested in the CLI or the R support). --- biology/Makefile | 1 + biology/erminej/Makefile | 29 +++++++++++++++++++++++++ biology/erminej/distinfo | 3 +++ biology/erminej/files/ermineJ.in | 17 +++++++++++++++ biology/erminej/files/patch-bin_forehead.conf | 18 ++++++++++++++++ biology/erminej/pkg-descr | 8 +++++++ biology/erminej/pkg-plist | 31 +++++++++++++++++++++++++++ 7 files changed, 107 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index f02dc903a129..60ab10072e29 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -32,6 +32,7 @@ SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss + SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 diff --git a/biology/erminej/Makefile b/biology/erminej/Makefile new file mode 100644 index 000000000000..39c19e7d2a25 --- /dev/null +++ b/biology/erminej/Makefile @@ -0,0 +1,29 @@ +PORTNAME= erminej +DISTVERSION= 3.2 +CATEGORIES= biology java +MASTER_SITES= http://home.pavlab.msl.ubc.ca/ermineJ/distributions/ +DISTNAME= ermineJ-${DISTVERSION}-generic-bundle + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Analyses of gene sets such as gene expression profiling studies + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +USES= zip +USE_JAVA= yes + +WRKSRC= ${WRKDIR}/ermineJ-${DISTVERSION} +NO_BUILD= yes +NO_ARCH= yes + +SUB_FILES= ermineJ +SUB_LIST= JAVA_HOME=${JAVA_HOME} + +do-install: + cd ${WRKSRC}/lib && ${COPYTREE_SHARE} . \ + ${STAGEDIR}${JAVAJARDIR}/${PORTNAME} + ${INSTALL_SCRIPT} ${WRKDIR}/ermineJ ${STAGEDIR}${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/bin/forehead.conf ${STAGEDIR}${PREFIX}/etc + +.include <bsd.port.mk> diff --git a/biology/erminej/distinfo b/biology/erminej/distinfo new file mode 100644 index 000000000000..8e979af904bd --- /dev/null +++ b/biology/erminej/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1625698692 +SHA256 (ermineJ-3.2-generic-bundle.zip) = 6e711b100e7619863ad2730714cdfa466115b563c146cb20a30488780504d5ac +SIZE (ermineJ-3.2-generic-bundle.zip) = 14314004 diff --git a/biology/erminej/files/ermineJ.in b/biology/erminej/files/ermineJ.in new file mode 100755 index 000000000000..f53de8eb4354 --- /dev/null +++ b/biology/erminej/files/ermineJ.in @@ -0,0 +1,17 @@ +#!/bin/sh + +ERMINEJ_HOME=%%JAVAJARDIR%%/erminej +ERMINEJ_ETC=%%PREFIX%%/etc +JAVA_HOME=%%JAVA_HOME%% +JAVACMD=$JAVA_HOME/bin/java + +MAIN_CLASS=com.werken.forehead.Forehead + +set -x +"$JAVACMD" \ + -Xmx3g \ + -Djavax.xml.parsers.SAXParserFactory=org.apache.xerces.jaxp.SAXParserFactoryImpl \ + -classpath "$ERMINEJ_HOME/forehead.jar" \ + "-Dforehead.conf.file=$ERMINEJ_ETC/forehead.conf" \ + "-DermineJ.home=$ERMINEJ_HOME" \ + $MAIN_CLASS "$@" diff --git a/biology/erminej/files/patch-bin_forehead.conf b/biology/erminej/files/patch-bin_forehead.conf new file mode 100644 index 000000000000..38a18bcef949 --- /dev/null +++ b/biology/erminej/files/patch-bin_forehead.conf @@ -0,0 +1,18 @@ +--- bin/forehead.conf.orig 2021-07-08 00:06:39 UTC ++++ bin/forehead.conf +@@ -7,12 +7,12 @@ + =[root.ermineJCmd] ubic.erminej.ErmineJCli + + [root] +- ${ermineJ.home}/lib/*.jar ++ ${ermineJ.home}/*.jar + + [root.ermineJ] +- ${ermineJ.home}/lib/*.jar ++ ${ermineJ.home}/*.jar + + + [root.ermineJCmd] +- ${ermineJ.home}/lib/*.jar ++ ${ermineJ.home}/*.jar + diff --git a/biology/erminej/pkg-descr b/biology/erminej/pkg-descr new file mode 100644 index 000000000000..94ccbf50a01b --- /dev/null +++ b/biology/erminej/pkg-descr @@ -0,0 +1,8 @@ +ErmineJ performs analyses of gene sets in high-throughput genomics data such as +gene expression profiling studies. A typical goal is to determine whether +particular biological pathways are "doing something interesting" in an +experiment that generates long lists of candidates. The software is designed to +be used by biologists with little or no informatics background (but if you do, +you might be interested in the CLI or the R support). + +WWW: https://erminej.msl.ubc.ca/ diff --git a/biology/erminej/pkg-plist b/biology/erminej/pkg-plist new file mode 100644 index 000000000000..132aa436cbd7 --- /dev/null +++ b/biology/erminej/pkg-plist @@ -0,0 +1,31 @@ +bin/ermineJ +etc/forehead.conf +%%JAVAJARDIR%%/erminej/antlr.jar +%%JAVAJARDIR%%/erminej/baseCode.jar +%%JAVAJARDIR%%/erminej/colt.jar +%%JAVAJARDIR%%/erminej/commons-beanutils.jar +%%JAVAJARDIR%%/erminej/commons-cli.jar +%%JAVAJARDIR%%/erminej/commons-collections.jar +%%JAVAJARDIR%%/erminej/commons-configuration.jar +%%JAVAJARDIR%%/erminej/commons-io.jar +%%JAVAJARDIR%%/erminej/commons-lang3.jar +%%JAVAJARDIR%%/erminej/commons-logging.jar +%%JAVAJARDIR%%/erminej/commons-math3.jar +%%JAVAJARDIR%%/erminej/commons-net.jar +%%JAVAJARDIR%%/erminej/ermineJ.jar +%%JAVAJARDIR%%/erminej/forehead.jar +%%JAVAJARDIR%%/erminej/gemma-core.jar +%%JAVAJARDIR%%/erminej/gemma-gsec.jar +%%JAVAJARDIR%%/erminej/javax.activation-api.jar +%%JAVAJARDIR%%/erminej/jaxb-api.jar +%%JAVAJARDIR%%/erminej/jcl-over-slf4j.jar +%%JAVAJARDIR%%/erminej/jcommon.jar +%%JAVAJARDIR%%/erminej/jfreechart.jar +%%JAVAJARDIR%%/erminej/jsontools-core.jar +%%JAVAJARDIR%%/erminej/log4j.jar +%%JAVAJARDIR%%/erminej/mtj.jar +%%JAVAJARDIR%%/erminej/opencsv.jar +%%JAVAJARDIR%%/erminej/slf4j-api.jar +%%JAVAJARDIR%%/erminej/slf4j-log4j12.jar +%%JAVAJARDIR%%/erminej/xercesImpl.jar +%%JAVAJARDIR%%/erminej/xml-apis.jar
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