# HG changeset patch
# User iuc
# Date 1432061814 14400
# Node ID dc30c8910c69ed86bfb08af58c5a327502dd2665

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09

diff -r 000000000000 -r dc30c8910c69 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 14:56:54 2015 -0400
@@ -0,0 +1,41 @@
+<tool_dependency>
+    <package name="atlas" version="3.11.11">
+        <install version="1.0">
+            <actions>
+                <!-- first action is always downloading -->
+                <action type="download_by_url" target_filename="ATLAS.tar.bz2">http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.11.11/atlas3.11.11.tar.bz2</action>
+
+                <action type="download_file">http://www.netlib.org/lapack/lapack-3.4.2.tgz</action>
+
+                <action type="shell_command">
+                # try to disable cpu throttling
+                if hash cpufreq-selector 2>/dev/null; then
+                    cpufreq-selector -g performance
+                elif hash cpupower 2>/dev/null; then
+                    cpupower frequency-set -g performance
+                else
+                    echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector'
+                    exit
+                fi
+                </action>
+                <action type="shell_command">
+                    mkdir build &amp;&amp;
+                    cd build &amp;&amp;
+                    mkdir $INSTALL_DIR/atlas/ &amp;&amp;
+                    ../configure -Fa alg -fPIC --prefix=$INSTALL_DIR/atlas/ --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz
+                </action>
+                <action type="shell_command">cd ./build &amp;&amp; make </action>
+                <action type="shell_command">cd ./build &amp;&amp; make install</action>
+
+                <action type="set_environment">
+                    <environment_variable name="ATLAS_LIB_DIR" action="set_to">$INSTALL_DIR/atlas/lib</environment_variable>
+                    <environment_variable name="ATLAS_INCLUDE_DIR" action="set_to">$INSTALL_DIR/atlas/include</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>ATLAS_LIB_DIR and ATLAS_INCLUDE_DIR (including libatlas.a) will be exported for later use.
+        During ATLAS library compilation, ATLAS performs code efficiency checks. These checks can only provide optimal results, if "frequency scaling" is disabled on the CPU, and no other load-intense processes are running.
+        Ideally, you should compile on an empty cluster node with CPU frequency scaling disabled (see "cpufreq-selector" or "cpufreq-set").
+        </readme>
+    </package>
+</tool_dependency>