Mercurial > repos > iuc > package_atlas_3_10

annotate tool_dependencies.xml @ 4:f27d2f8761ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
author iuc
date Tue, 16 Feb 2016 16:57:05 -0500
parents 0538fd672119
children c0a66ce2a119
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f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="atlas" version="3.10.2">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action type="download_by_url" sha256sum="c36a9edf352aa3652ae2c3cccf752351e12291c1d018da842093f9dc70fa2da3">
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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8 https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz
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9 </action>
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10 <action type="move_directory_files">
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11 <source_directory>.</source_directory>
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12 <destination_directory>$INSTALL_DIR</destination_directory>
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
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16 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
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17 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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18 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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19 <environment_variable action="set_to" name="ATLAS">$INSTALL_DIR</environment_variable>
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20 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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21 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
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22 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
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23 </action>
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24 <action type="shell_command"><![CDATA[
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25 command -v gfortran || return 0
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26 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &&
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27 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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28 echo 'program test; end program test' > test.f90 &&
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29 gfortran -o test test.f90 &&
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30 LGF=`ldd test | grep libgfortran | awk '{print $3}'` &&
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31 LGF_CANON=`readlink -f $LGF` &&
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32 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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33 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
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34 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &&
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35 cp -p $LGF_CANON $BUNDLED_LGF_CANON
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36 fi
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37 ]]></action>
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38 </actions>
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39 <actions architecture="x86_64" os="darwin">
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40 <!-- NOOP: On OS X we will use Apple's vecLib -->
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41 </actions>
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42 <actions>
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43 <action type="download_file" sha256sum="3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f">
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44 https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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45 </action>
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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46 <action type="download_file" sha256sum="9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352">
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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47 https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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48 </action>
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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49 <action type="download_file" sha256sum="adbe462b179a2d626cd229cddcb08e39ae2f2544eccf80ab617790b307667146">
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50 https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff
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51 </action>
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52 <action type="download_file" sha256sum="95862478f7d276f948a58c583acd2935ada9ad3bb55944a303d94e161e202d89">
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53 https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff
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54 </action>
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
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55 <action type="download_file" sha256sum="f805600c46719f74752e9026e1461d084a385ba67838364a81c36cdfb69cad82">
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56 https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff
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57 </action>
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58 <action type="shell_command">tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2</action>
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59 <!-- a 64-bit architecture is assumed for compilation -->
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60 <action type="shell_command"><![CDATA[
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61 cd ATLAS &&
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62 mkdir ATLAS/build &&
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63 patch -p1 </host/static_full_blas_lapack.diff &&
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64 patch -p1 </host/shared_libraries.diff &&
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65 patch -p1 </host/cpu-throttling-check.diff &&
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66 cd build &&
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67 ../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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68 make &&
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69 make install
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70 ]]></action>
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71 <action type="set_environment">
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72 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
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73 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
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74 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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75 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
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76 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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77 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
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78 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
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79 </action>
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80 </actions>
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81 </actions_group>
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82 </install>
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83 <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR.
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84 This ATLAS build includes patches from the Debian ATLAS packages which enable additional features:
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85 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions
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86 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories
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87 This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$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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88 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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89 </readme>
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90 </package>
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91 </tool_dependency>