changeset 62:f9c068c8a80a

Uploaded

--- a/tool_dependencies.xml	Mon Aug 26 17:14:20 2013 -0400
+++ b/tool_dependencies.xml	Fri Sep 20 06:30:04 2013 -0400
@@ -1,36 +1,42 @@
-<?xml version="1.0"?>
 <tool_dependency>
-    <package name="blast+" version="2.2.26+">
+    <package name="atlas" version="3.10.1">
         <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/Stable/3.10.1/atlas3.10.1.tar.bz2</action>
+<!--                <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.1.tar.bz2</action>
+                <action type="shell_command">tar xfvj atlas3.10.1.tar.bz2</action>-->
+                <action type="download_file">http://www.netlib.org/lapack/lapack-3.4.2.tgz</action>
 
-            <action type="download_binary">
-                <url_template architecture="x86_64" os="linux">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</url_template>
-                <url_template architecture="i386" os="linux">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template>
-                <url_template architecture="i686" os="linux">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template>
-                <url_template architecture="i686" os="darwin">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</url_template>
-                <url_template architecture="i386" os="darwin">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</url_template>
-                <url_template architecture="x86_64" os="darwin">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</url_template>
-            </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="shell_command">
-                tar -zxvf $INSTALL_DIR/ncbi-blast-2.2.26+-x64-linux.tar.gz ;
-                tar -zxvf $INSTALL_DIR/ncbi-blast-2.2.26+-ia32-linux.tar.gz ;
-                tar -zxvf $INSTALL_DIR/ncbi-blast-2.2.26+-universal-macosx.tar.gz ;
-            </action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <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>
-Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
-binaries from the NCBI, which is faster than performing a local compliation,
-avoids any issues with build dependencies, and is more reproducible between
-installations as there is no variability from the compiler or library versions.
-
-For more details, see:
-http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
+        <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>