Merge pull request #547 from TheJacksonLaboratory/develop

Develop

.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,20 @@
+#
+# The Exomiser - A tool to annotate and prioritize genomic variants
+#
+# Copyright (c) 2016-2018 Queen Mary University of London.
+# Copyright (c) 2012-2016 Charit� Universit�tsmedizin Berlin and Genome Research Ltd.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.6.0/apache-maven-3.6.0-bin.zip

CHANGELOG.rst

@@ -2,6 +2,19 @@
 Changelog
 =========
 
+-------------------
+v1.3.2 (2021-04-09)
+-------------------
+- Fixed null pointer error in YAML output
+
+------
+v1.3.1
+------
+- Update download URL for phenotype.hpoa
+- Update versions of multiple plugins/dependencies
+- Add option to simultaneously output HTML and TSV
+- maven wrapper
+
 ------
 v1.3.0
 ------

docs/yaml-vcf.rst

@@ -46,7 +46,7 @@ Any of the options described in :ref:`rstyamlhpo` can also be used here.
 
 Additionally, ``hpoIds`` is a list of HPO term representing the clinical manifestations observed in the individual being analyzed.
 Finally,  ``prefix`` is the prefix of the output file (optional, default: lirical) For instance, if the prefix is ``example1``, then the HTML output file will be
-``example1.html``.
+``example1.html``. ``prefix`` is *not* used to represent the path to the outfile.
 
 
 The following YAML file contains values for all of the options. ::

mvnw

@@ -0,0 +1,225 @@
+#!/bin/sh
+# ----------------------------------------------------------------------------
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+# ----------------------------------------------------------------------------
+
+# ----------------------------------------------------------------------------
+# Maven2 Start Up Batch script
+#
+# Required ENV vars:
+# ------------------
+#   JAVA_HOME - location of a JDK home dir
+#
+# Optional ENV vars
+# -----------------
+#   M2_HOME - location of maven2's installed home dir
+#   MAVEN_OPTS - parameters passed to the Java VM when running Maven
+#     e.g. to debug Maven itself, use
+#       set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
+#   MAVEN_SKIP_RC - flag to disable loading of mavenrc files
+# ----------------------------------------------------------------------------
+
+if [ -z "$MAVEN_SKIP_RC" ] ; then
+
+  if [ -f /etc/mavenrc ] ; then
+    . /etc/mavenrc
+  fi
+
+  if [ -f "$HOME/.mavenrc" ] ; then
+    . "$HOME/.mavenrc"
+  fi
+
+fi
+
+# OS specific support.  $var _must_ be set to either true or false.
+cygwin=false;
+darwin=false;
+mingw=false
+case "`uname`" in
+  CYGWIN*) cygwin=true ;;
+  MINGW*) mingw=true;;
+  Darwin*) darwin=true
+    # Use /usr/libexec/java_home if available, otherwise fall back to /Library/Java/Home
+    # See https://developer.apple.com/library/mac/qa/qa1170/_index.html
+    if [ -z "$JAVA_HOME" ]; then
+      if [ -x "/usr/libexec/java_home" ]; then
+        export JAVA_HOME="`/usr/libexec/java_home`"
+      else
+        export JAVA_HOME="/Library/Java/Home"
+      fi
+    fi
+    ;;
+esac
+
+if [ -z "$JAVA_HOME" ] ; then
+  if [ -r /etc/gentoo-release ] ; then
+    JAVA_HOME=`java-config --jre-home`
+  fi
+fi
+
+if [ -z "$M2_HOME" ] ; then
+  ## resolve links - $0 may be a link to maven's home
+  PRG="$0"
+
+  # need this for relative symlinks
+  while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+      PRG="$link"
+    else
+      PRG="`dirname "$PRG"`/$link"
+    fi
+  done
+
+  saveddir=`pwd`
+
+  M2_HOME=`dirname "$PRG"`/..
+
+  # make it fully qualified
+  M2_HOME=`cd "$M2_HOME" && pwd`
+
+  cd "$saveddir"
+  # echo Using m2 at $M2_HOME
+fi
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+  [ -n "$M2_HOME" ] &&
+    M2_HOME=`cygpath --unix "$M2_HOME"`
+  [ -n "$JAVA_HOME" ] &&
+    JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+  [ -n "$CLASSPATH" ] &&
+    CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
+fi
+
+# For Migwn, ensure paths are in UNIX format before anything is touched
+if $mingw ; then
+  [ -n "$M2_HOME" ] &&
+    M2_HOME="`(cd "$M2_HOME"; pwd)`"
+  [ -n "$JAVA_HOME" ] &&
+    JAVA_HOME="`(cd "$JAVA_HOME"; pwd)`"
+  # TODO classpath?
+fi
+
+if [ -z "$JAVA_HOME" ]; then
+  javaExecutable="`which javac`"
+  if [ -n "$javaExecutable" ] && ! [ "`expr \"$javaExecutable\" : '\([^ ]*\)'`" = "no" ]; then
+    # readlink(1) is not available as standard on Solaris 10.
+    readLink=`which readlink`
+    if [ ! `expr "$readLink" : '\([^ ]*\)'` = "no" ]; then
+      if $darwin ; then
+        javaHome="`dirname \"$javaExecutable\"`"
+        javaExecutable="`cd \"$javaHome\" && pwd -P`/javac"
+      else
+        javaExecutable="`readlink -f \"$javaExecutable\"`"
+      fi
+      javaHome="`dirname \"$javaExecutable\"`"
+      javaHome=`expr "$javaHome" : '\(.*\)/bin'`
+      JAVA_HOME="$javaHome"
+      export JAVA_HOME
+    fi
+  fi
+fi
+
+if [ -z "$JAVACMD" ] ; then
+  if [ -n "$JAVA_HOME"  ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+      # IBM's JDK on AIX uses strange locations for the executables
+      JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+      JAVACMD="$JAVA_HOME/bin/java"
+    fi
+  else
+    JAVACMD="`which java`"
+  fi
+fi
+
+if [ ! -x "$JAVACMD" ] ; then
+  echo "Error: JAVA_HOME is not defined correctly." >&2
+  echo "  We cannot execute $JAVACMD" >&2
+  exit 1
+fi
+
+if [ -z "$JAVA_HOME" ] ; then
+  echo "Warning: JAVA_HOME environment variable is not set."
+fi
+
+CLASSWORLDS_LAUNCHER=org.codehaus.plexus.classworlds.launcher.Launcher
+
+# traverses directory structure from process work directory to filesystem root
+# first directory with .mvn subdirectory is considered project base directory
+find_maven_basedir() {
+
+  if [ -z "$1" ]
+  then
+    echo "Path not specified to find_maven_basedir"
+    return 1
+  fi
+
+  basedir="$1"
+  wdir="$1"
+  while [ "$wdir" != '/' ] ; do
+    if [ -d "$wdir"/.mvn ] ; then
+      basedir=$wdir
+      break
+    fi
+    # workaround for JBEAP-8937 (on Solaris 10/Sparc)
+    if [ -d "${wdir}" ]; then
+      wdir=`cd "$wdir/.."; pwd`
+    fi
+    # end of workaround
+  done
+  echo "${basedir}"
+}
+
+# concatenates all lines of a file
+concat_lines() {
+  if [ -f "$1" ]; then
+    echo "$(tr -s '\n' ' ' < "$1")"
+  fi
+}
+
+BASE_DIR=`find_maven_basedir "$(pwd)"`
+if [ -z "$BASE_DIR" ]; then
+  exit 1;
+fi
+
+export MAVEN_PROJECTBASEDIR=${MAVEN_BASEDIR:-"$BASE_DIR"}
+echo $MAVEN_PROJECTBASEDIR
+MAVEN_OPTS="$(concat_lines "$MAVEN_PROJECTBASEDIR/.mvn/jvm.config") $MAVEN_OPTS"
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+  [ -n "$M2_HOME" ] &&
+    M2_HOME=`cygpath --path --windows "$M2_HOME"`
+  [ -n "$JAVA_HOME" ] &&
+    JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
+  [ -n "$CLASSPATH" ] &&
+    CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
+  [ -n "$MAVEN_PROJECTBASEDIR" ] &&
+    MAVEN_PROJECTBASEDIR=`cygpath --path --windows "$MAVEN_PROJECTBASEDIR"`
+fi
+
+WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
+
+exec "$JAVACMD" \
+  $MAVEN_OPTS \
+  -classpath "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" \
+  "-Dmaven.home=${M2_HOME}" "-Dmaven.multiModuleProjectDirectory=${MAVEN_PROJECTBASEDIR}" \
+  ${WRAPPER_LAUNCHER} $MAVEN_CONFIG "$@"