# HG changeset patch
# User deepakjadmin
# Date 1442994510 14400
# Node ID 6ce3b057cf508c226166a2743378fe8d3b6c505f
Uploaded
diff -r 000000000000 -r 6ce3b057cf50 testing.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testing.xml Wed Sep 23 03:48:30 2015 -0400
@@ -0,0 +1,15 @@
+
+ R version and installation test
+
+ R_ROOT_DIR
+ R
+
+ /bin/which R > $output_file;
+ /bin/which \$R_ROOT_DIR/bin/R >> $output_file;
+ echo \$R_ROOT_DIR >> $output_file;
+ echo \$PATH >> $output_file;
+
+
+
+
+
diff -r 000000000000 -r 6ce3b057cf50 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Sep 23 03:48:30 2015 -0400
@@ -0,0 +1,120 @@
+
+
+
+
+
+
+ https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz
+
+ .
+ $INSTALL_DIR
+
+
+
+ https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz
+
+ .
+ $INSTALL_DIR
+
+
+ $INSTALL_DIR/lib/libtcl8.4.so
+ $INSTALL_DIR/lib/libtk8.4.so
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIBS" &&
+ export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIBS" &&
+ export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &&
+ export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &&
+ export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &&
+ export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &&
+ export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &&
+ export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &&
+ ./configure --with-tcltk \
+ --with-blas \
+ --with-lapack \
+ --with-readline \
+ --with-cairo \
+ --with-libpng \
+ --without-x \
+ --enable-R-shlib \
+ --disable-R-framework \
+ --libdir=$INSTALL_DIR/lib \
+ --prefix=$INSTALL_DIR
+
+
+ sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R
+ sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R
+
+
+ $INSTALL_DIR/lib/R/doc
+ $INSTALL_DIR/lib/R
+ $INSTALL_DIR/lib/R/include
+ $INSTALL_DIR/lib/R/share
+ $INSTALL_DIR
+ $INSTALL_DIR/lib/R
+ $INSTALL_DIR/lib/R
+ $INSTALL_DIR/lib/R/library
+ $INSTALL_DIR/bin
+
+
+
+
+ The precompiled versions of this package were built 2014-03-06.
+ R is a free software environment for statistical computing and graphics.
+ NOTE: See custom compilation options above.
+
+
+
+
+
+
+
+
+
+
+ http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.24.15.tar.gz
+ R CMD INSTALL limma_3.24.15.tar.gz
+
+
+
+
+limma_3.24.12 installed now try edgeR
+
+
+
+
+