# HG changeset patch
# User iuc
# Date 1437039822 14400
# Node ID 0538fd6721193ccdf3fc4684c741112366b27bbd
# Parent  b36c9ee883e909c9e479e9dd41769fc6ec5a5844
Uploaded

diff -r b36c9ee883e9 -r 0538fd672119 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat May 23 16:52:20 2015 -0400
+++ b/tool_dependencies.xml	Thu Jul 16 05:43:42 2015 -0400
@@ -15,7 +15,22 @@
                         <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
                         <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                         <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
+                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
                     </action>
+                    <action type="shell_command"><![CDATA[
+                        command -v gfortran || return 0
+                        BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &&
+                        BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
+                        echo 'program test; end program test' > test.f90 &&
+                        gfortran -o test test.f90 &&
+                        LGF=`ldd test | grep libgfortran | awk '{print $3}'` &&
+                        LGF_CANON=`readlink -f $LGF` &&
+                        LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
+                        if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
+                            cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &&
+                            cp -p $LGF_CANON $BUNDLED_LGF_CANON
+                        fi
+                    ]]></action>
                 </actions>
                 <actions architecture="x86_64" os="darwin">
                     <!-- NOOP: On OS X we will use Apple's vecLib -->
@@ -28,17 +43,17 @@
                     <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action>
                     <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action>
                     <!-- a 64-bit architecture is assumed for compilation -->
-                    <action type="shell_command">
-                        cd ATLAS &amp;&amp;
-                        mkdir ATLAS/build &amp;&amp;
-                        patch -p1 &lt;/host/static_full_blas_lapack.diff &amp;&amp;
-                        patch -p1 &lt;/host/shared_libraries.diff &amp;&amp;
-                        patch -p1 &lt;/host/cpu-throttling-check.diff &amp;&amp;
-                        cd build &amp;&amp;
-                        ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 &amp;&amp;
-                        make &amp;&amp;
+                    <action type="shell_command"><![CDATA[
+                        cd ATLAS &&
+                        mkdir ATLAS/build &&
+                        patch -p1 </host/static_full_blas_lapack.diff &&
+                        patch -p1 </host/shared_libraries.diff &&
+                        patch -p1 </host/cpu-throttling-check.diff &&
+                        cd build &&
+                        ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 &&
+                        make &&
                         make install
-                    </action>
+                    ]]></action>
                     <action type="set_environment">
                         <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
                         <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>