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1 <tool_dependency>
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1
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2 <package name="atlas" version="3.10.2">
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3 <install version="1.0">
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4 <actions_group>
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5 <actions architecture="x86_64" os="linux">
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6 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/atlas/atlas-3.10.2-Linux-x86_64.tar.gz</action>
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7 <action type="move_directory_files">
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8 <source_directory>.</source_directory>
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9 <destination_directory>$INSTALL_DIR</destination_directory>
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10 </action>
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11 <action type="set_environment">
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12 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
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13 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
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14 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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15 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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16 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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17 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
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18 </action>
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19 </actions>
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20 <actions architecture="x86_64" os="darwin">
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21 <!-- NOOP: On OS X we will use Apple's vecLib -->
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22 </actions>
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23 <actions>
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24 <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action>
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25 <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action>
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26 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action>
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27 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action>
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28 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action>
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29 <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action>
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30 <!-- a 64-bit architecture is assumed for compilation -->
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31 <action type="shell_command">
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32 cd ATLAS &&
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33 mkdir ATLAS/build &&
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34 patch -p1 </host/static_full_blas_lapack.diff &&
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35 patch -p1 </host/shared_libraries.diff &&
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36 patch -p1 </host/cpu-throttling-check.diff &&
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37 cd build &&
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38 ../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 &&
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39 make &&
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40 make install
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41 </action>
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42 <action type="set_environment">
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43 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
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44 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
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45 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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46 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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47 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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48 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
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49 </action>
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50 </actions>
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51 </actions_group>
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52 </install>
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53 <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR.
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54 This ATLAS build includes patches from the Debian ATLAS packages which enable additional features:
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55 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions
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56 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories
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57 This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$ATLAS_LIB_DIR so that any dependent packages which link to ATLAS will be able to resolve all necessary libraries at runtime.
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58 On Mac OS X, this package is a dummy package - BLAS and LAPACK libraries are already provided in Apple's vecLib.
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59 </readme>
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60 </package>
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61 </tool_dependency>
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