Mercurial > repos > iuc > package_atlas_3_11

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 14:56:54 -0400
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dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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1 <tool_dependency>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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2 <package name="atlas" version="3.11.11">
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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3 <install version="1.0">
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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4 <actions>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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5 <!-- first action is always downloading -->
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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6 <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>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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7
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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8 <action type="download_file">http://www.netlib.org/lapack/lapack-3.4.2.tgz</action>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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9
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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10 <action type="shell_command">
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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11 # try to disable cpu throttling
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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12 if hash cpufreq-selector 2>/dev/null; then
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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13 cpufreq-selector -g performance
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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14 elif hash cpupower 2>/dev/null; then
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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15 cpupower frequency-set -g performance
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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16 else
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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17 echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector'
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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18 exit
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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19 fi
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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20 </action>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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21 <action type="shell_command">
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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22 mkdir build &amp;&amp;
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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23 cd build &amp;&amp;
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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24 mkdir $INSTALL_DIR/atlas/ &amp;&amp;
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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25 ../configure -Fa alg -fPIC --prefix=$INSTALL_DIR/atlas/ --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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26 </action>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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27 <action type="shell_command">cd ./build &amp;&amp; make </action>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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28 <action type="shell_command">cd ./build &amp;&amp; make install</action>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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29
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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30 <action type="set_environment">
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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31 <environment_variable name="ATLAS_LIB_DIR" action="set_to">$INSTALL_DIR/atlas/lib</environment_variable>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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32 <environment_variable name="ATLAS_INCLUDE_DIR" action="set_to">$INSTALL_DIR/atlas/include</environment_variable>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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33 </action>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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34 </actions>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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35 </install>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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36 <readme>ATLAS_LIB_DIR and ATLAS_INCLUDE_DIR (including libatlas.a) will be exported for later use.
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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37 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.
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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38 Ideally, you should compile on an empty cluster node with CPU frequency scaling disabled (see "cpufreq-selector" or "cpufreq-set").
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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39 </readme>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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40 </package>
dc30c8910c69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_11 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
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41 </tool_dependency>