# HG changeset patch
# User morinlab
# Date 1480890708 18000
# Node ID b5ab09203060e009192ba56df1c271529dcbe6d2
# Parent  47e78ffd147ea73149950756d1cb83c05ab23f76
Uploaded

diff -r 47e78ffd147e -r b5ab09203060 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Dec 04 17:30:17 2016 -0500
+++ b/tool_dependencies.xml	Sun Dec 04 17:31:48 2016 -0500
@@ -1,97 +1,76 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R" version="3.1.2">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action sha256sum="586dde39d6821bcc5079004450f5d19f836a26d4554083c7add3933f071451e0" type="download_by_url">https://depot.galaxyproject.org/software/r/r_3.1.2_linux_x64.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                    <action type="set_environment">
-                        <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
-                        <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
-                    </action>
-                </actions>
-                <actions>
-                    <action sha256sum="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a" type="download_by_url">https://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action>
-                    <package name="readline" version="6.2">
-                        <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="libpng" version="1.6.7">
-                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="cairo" version="1.12.14">
-                        <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="pixman" version="0.32.4">
-                        <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="freetype" version="2.5.2">
-                        <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="ncurses" version="5.9">
-                        <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="fontconfig" version="2.11.1">
-                        <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-                    </package>
-                    <action type="set_environment_for_install">
-                        <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                            <package name="readline" version="6.2" />
-                        </repository>
-                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                            <package name="libpng" version="1.6.7" />
-                        </repository>
-                        <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                            <package name="cairo" version="1.12.14" />
-                        </repository>
-                        <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                            <package name="pixman" version="0.32.4" />
-                        </repository>
-                        <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                            <package name="freetype" version="2.5.2" />
-                        </repository>
-                        <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                            <package name="ncurses" version="5.9" />
-                        </repository>
-                        <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                            <package name="fontconfig" version="2.11.1" />
-                        </repository>
-                    </action>
-                    <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action>
-                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
-                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
-                </actions>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
-                    <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
-                    <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
-                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <!-- Include library with local rJava installation -->
-                    <environment_variable action="prepend_to" name="R_LIBS">/usr/lib/R/site-library</environment_variable>
-                    <!-- Set JAVA_HOME & LD_LIBRARY_PATH -->
-                    <environment_variable action="set_to" name="JAVA_HOME">/usr/lib/jvm/java-8-openjdk-amd64/jre</environment_variable>
-                    <environment_variable action="set_to" name="LD_LIBRARY_PATH">/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server</environment_variable>
-                    <!-- Set FONTCONFIG_PATH for R png output -->
-                    <environment_variable action="set_to" name="FONTCONFIG_PATH">$INSTALL_DIR/etc/fonts</environment_variable>
-                    <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
-                    <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <!-- Append java bin to PATH -->
-                    <environment_variable action="append_to" name="PATH">$JAVA_HOME/bin</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>
-                The precompiled versions of this package were built 2014-12-21.
-                R is a free software environment for statistical computing and graphics.
-                NOTE: See custom compilation options above.
-        </readme>
-    </package>
+
+	<!-- R -->
+	<package name="R" version="3.1.2">
+		<repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />	
+	</package>
+
+	<!-- Morinlab scripts with EXPANDS wrapper script -->
+	<package name="morinlab_scripts" version="14.2">
+		<repository changeset_revision="b88b230de028" name="package_morinlab_scripts_14_2" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+	</package>
+	
+	<!-- EXPANDS and other R packages -->
+	<package name="expands" version="1.7.2">
+
+		<install version="1.0">
+		<actions>
+
+			<action type="set_environment_for_install">
+				<repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
+					<package name="R" version="3.1.2" />
+				</repository>
+			</action>
+
+			<action type="shell_command">R CMD javareconf -e</action>
+
+ 			<action type="setup_r_environment">
+				<repository changeset_revision="d2f70822dc31" name="package_r_3_1_2_rjava" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">	
+					<package name="R" version="3.1.2" />	
+				</repository>
+				<package>https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/mclust_5.2.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/nnet/nnet_7.3-11.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/flexmix_2.3-13.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/nlme/nlme_3.1-122.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/ape_3.5.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/permute_0.9-0.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/moments_0.14.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/argparser_0.4.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/matlab_1.0.2.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/digest/digest_0.6.9.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_0.12.5.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.8.3.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/stringi/stringi_1.0-1.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/stringr/stringr_0.6.2.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/reshape2/reshape2_1.4.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/munsell/munsell_0.4.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/scales/scales_0.3.0.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/ggrepel_0.5.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/DBI/DBI_0.4-1.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/R6/R6_2.1.1.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/Archive/BH/BH_1.60.0-1.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz</package>
+				<package>https://cran.r-project.org/src/contrib/expands_1.7.2.tar.gz</package>
+			</action>
+		</actions>
+
+		</install>
+
+	</package>
+	<readme>
+	Expanding Ploidy and Allele Frequency on Nested Subpopulations (EXPANDS) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome-sequencing input data.
+	</readme>
 </tool_dependency>