From owner-dev-commits-ports-all@freebsd.org Fri Jul 9 12:29:14 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 9F78165F390; Fri, 9 Jul 2021 12:29:14 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4GLssk2Gvkz4td9; Fri, 9 Jul 2021 12:29:14 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 3216D1487C; Fri, 9 Jul 2021 12:29:14 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 169CTEU6083785; Fri, 9 Jul 2021 12:29:14 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 169CTEIj083784; Fri, 9 Jul 2021 12:29:14 GMT (envelope-from git) Date: Fri, 9 Jul 2021 12:29:14 GMT Message-Id: <202107091229.169CTEIj083784@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: e44f917e298a - main - biology/erminej: Analyses of gene sets, e.g. gene expression profiling MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e44f917e298a1f860fab0790aacd348cae60f74b Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 09 Jul 2021 12:29:14 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=e44f917e298a1f860fab0790aacd348cae60f74b commit e44f917e298a1f860fab0790aacd348cae60f74b Author: Jason W. Bacon AuthorDate: 2021-07-09 12:26:58 +0000 Commit: Jason W. Bacon 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 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