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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">$INSTALL_DIR/lib</environment_variable>
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18 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
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19 </action>
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20 <action type="shell_command"><![CDATA[
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21 command -v gfortran || return 0
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22 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &&
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23 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
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24 echo 'program test; end program test' > test.f90 &&
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25 gfortran -o test test.f90 &&
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26 LGF=`ldd test | grep libgfortran | awk '{print $3}'` &&
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27 LGF_CANON=`readlink -f $LGF` &&
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28 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
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29 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
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30 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &&
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31 cp -p $LGF_CANON $BUNDLED_LGF_CANON
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32 fi
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33 ]]></action>
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34 </actions>
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35 <actions architecture="x86_64" os="darwin">
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36 <!-- NOOP: On OS X we will use Apple's vecLib -->
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37 </actions>
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38 <actions>
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39 <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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40 <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action>
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41 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action>
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42 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action>
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43 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action>
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44 <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action>
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45 <!-- a 64-bit architecture is assumed for compilation -->
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46 <action type="shell_command"><![CDATA[
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47 cd ATLAS &&
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48 mkdir ATLAS/build &&
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49 patch -p1 </host/static_full_blas_lapack.diff &&
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50 patch -p1 </host/shared_libraries.diff &&
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51 patch -p1 </host/cpu-throttling-check.diff &&
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52 cd build &&
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53 ../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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54 make &&
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55 make install
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56 ]]></action>
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57 <action type="set_environment">
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58 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
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59 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
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60 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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61 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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62 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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63 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
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64 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
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65 </action>
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66 </actions>
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67 </actions_group>
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68 </install>
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69 <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR.
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70 This ATLAS build includes patches from the Debian ATLAS packages which enable additional features:
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71 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions
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72 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories
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73 This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$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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74 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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75 </readme>
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76 </package>
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77 </tool_dependency>
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