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).

7 files changed, 107 insertions, 0 deletions

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