add new beast2 version (2.6.0)

recipes/beast2/beast_lib.patch

@@ -0,0 +1,123 @@
+diff --git a/beast/bin/applauncher b/beast/bin/applauncher
+index 5ac941f..e0a92c2 100755
+--- a/beast/bin/applauncher
++++ b/beast/bin/applauncher
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java
+diff --git a/beast/bin/beast b/beast/bin/beast
+index 73c83b0..3d147b6 100755
+--- a/beast/bin/beast
++++ b/beast/bin/beast
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java
+@@ -38,15 +38,16 @@ if [ -n "$BEAGLE_LIB" ]; then
+ 	else
+ 		BEAST_EXTRA_LIBS=$BEAGLE_LIB
+ 	fi
++BEAST_EXTRA_LIBS=${BEAST_EXTRA_LIBS}:${PREFIX}/lib
+ fi
+
+ # Explicitly add /usr/local/lib to library search path to ensure 
+ # beast continues to find beagle when installed here.  (This is
+ # necessary due to known problems with certain JREs.)
+ if [ -z "$LD_LIBRARY_PATH" ]; then
+-    export LD_LIBRARY_PATH=/usr/local/lib
++    export LD_LIBRARY_PATH=${PREFIX}/lib
+ else
+-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":/usr/local/lib
++    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":${PREFIX}/lib
+ fi
+
+ # use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations 
+diff --git a/beast/bin/beauti b/beast/bin/beauti
+index c8046d6..e30ee8b 100755
+--- a/beast/bin/beauti
++++ b/beast/bin/beauti
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java
+diff --git a/beast/bin/densitree b/beast/bin/densitree
+index 97f0ac9..c7f5178 100755
+--- a/beast/bin/densitree
++++ b/beast/bin/densitree
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java
+diff --git a/beast/bin/loganalyser b/beast/bin/loganalyser
+index f5dada1..7f2aa07 100755
+--- a/beast/bin/loganalyser
++++ b/beast/bin/loganalyser
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java
+diff --git a/beast/bin/logcombiner b/beast/bin/logcombiner
+index d227029..dc1e8b3 100755
+--- a/beast/bin/logcombiner
++++ b/beast/bin/logcombiner
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java
+diff --git a/beast/bin/packagemanager b/beast/bin/packagemanager
+index 5329e35..5bf7864 100755
+--- a/beast/bin/packagemanager
++++ b/beast/bin/packagemanager
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java
+diff --git a/beast/bin/treeannotator b/beast/bin/treeannotator
+index 0f178e0..2aa3d6d 100755
+--- a/beast/bin/treeannotator
++++ b/beast/bin/treeannotator
+@@ -22,7 +22,7 @@ if [ -z "$BEAST" ]; then
+ 	cd "$saveddir"
+ fi
+
+-BEAST_LIB="$BEAST/lib"
++BEAST_LIB="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib"
+
+ if [ -z "$JAVA_HOME" ]; then
+   JAVA=java

recipes/beast2/build.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin ${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}/lib
+for file in applauncher beast beauti densitree loganalyser logcombiner packagemanager treeannotator
+    do envsubst '${PREFIX}:${PKG_NAME}:${PKG_VERSION}:${PKG_BUILDNUM}' < bin/$file > ${PREFIX}/bin/$file
+    chmod +x ${PREFIX}/bin/$file
+done
+cp -R lib ${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}
+cp -R {examples,images,templates} ${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}

recipes/beast2/meta.yaml

@@ -0,0 +1,56 @@
+{% set name = 'beast2' %}
+{% set version = '2.6.0' %}
+{% set hash = 'b7ae682904cec3a0c33f7d8b2f9d840afe5c00a3f0db6bd7aade7cfd7629dd76' %}
+
+package:
+  name: '{{ name }}'
+  version: '{{ version }}'
+
+source:
+  url: 'https://github.com/CompEvol/beast2/releases/download/v2.6.0/BEAST.v2.6.0.Linux.tgz'
+  sha256: '{{ hash }}'
+  patches:
+    - beast_lib.patch
+
+build:
+  number: 0
+  noarch: generic
+
+requirements:
+  build:
+    - gettext
+
+  host:
+    - openjdk 8.0* zulu8*
+    - beagle-lib
+    - fontconfig
+    - font-ttf-ubuntu
+    - fontconfig
+    - freetype
+    - xorg-libxtst
+
+  run:
+    - openjdk 8.0* zulu8*
+    - beagle-lib
+    - fontconfig
+    - font-ttf-ubuntu
+    - fontconfig
+    - freetype
+    - xorg-libxtst
+
+test:
+  commands:
+    - beast -version
+    # check to make sure beagle-lib is loaded ok
+    - beast -beagle_info \| grep Flags
+    - applauncher -help
+    - packagemanager -help
+    - loganalyser -h
+    - logcombiner -help
+    - treeannotator -help
+
+about:
+  home: http://www.beast2.org
+  license: LGPLv2.1
+  license_file: LICENSE.txt
+  summary: "BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences."