Mercurial > repos > iuc > package_atlas_3_10
annotate tool_dependencies.xml @ 7:86b7c19454fa draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 15 Jul 2015 10:35:14 -0400 |
| parents | 4778b172b895 |
| children | c47756a8136e |
| rev | line source |
|---|---|
| 0 | 1 <tool_dependency> |
| 5 | 2 <package name="atlas" version="3.10.2"> |
| 0 | 3 <install version="1.0"> |
| 5 | 4 <actions_group> |
| 5 <actions architecture="x86_64" os="linux"> | |
| 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> | |
| 7 <action type="move_directory_files"> | |
| 8 <source_directory>.</source_directory> | |
| 9 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 10 </action> | |
| 11 <action type="set_environment"> | |
| 12 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> | |
| 13 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> | |
| 14 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
| 15 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
| 16 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 17 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> | |
| 7 | 18 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable> |
| 5 | 19 </action> |
| 7 | 20 <action type="shell_command"><![CDATA[ |
| 21 command -v gfortran || return 0 | |
| 22 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 && | |
| 23 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && | |
| 24 echo 'program test; end program test' > test.f90 && | |
| 25 gfortran -o test test.f90 && | |
| 26 LGF=`ldd test | grep libgfortran | awk '{print $3}'` && | |
| 27 LGF_CANON=`readlink -f $LGF` && | |
| 28 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && | |
| 29 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then | |
| 30 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled && | |
| 31 cp -p $LGF_CANON $BUNDLED_LGF_CANON | |
| 32 fi | |
| 33 ]]></action> | |
| 5 | 34 </actions> |
| 35 <actions architecture="x86_64" os="darwin"> | |
| 36 <!-- NOOP: On OS X we will use Apple's vecLib --> | |
| 37 </actions> | |
| 38 <actions> | |
| 39 <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action> | |
| 40 <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action> | |
| 41 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action> | |
| 42 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action> | |
| 43 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action> | |
| 44 <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action> | |
| 45 <!-- a 64-bit architecture is assumed for compilation --> | |
| 7 | 46 <action type="shell_command"><![CDATA[ |
| 47 cd ATLAS && | |
| 48 mkdir ATLAS/build && | |
| 49 patch -p1 </host/static_full_blas_lapack.diff && | |
| 50 patch -p1 </host/shared_libraries.diff && | |
| 51 patch -p1 </host/cpu-throttling-check.diff && | |
| 52 cd build && | |
| 53 ../configure --prefix="$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 && | |
| 54 make && | |
| 5 | 55 make install |
| 7 | 56 ]]></action> |
| 5 | 57 <action type="set_environment"> |
| 58 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> | |
| 59 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> | |
| 60 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
| 61 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
| 62 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 63 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> | |
|
6
4778b172b895
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 0d7fcf576fd797327af90538b216473ef13daa41
iuc
parents:
5
diff
changeset
|
64 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable> |
| 5 | 65 </action> |
| 66 </actions> | |
| 67 </actions_group> | |
| 0 | 68 </install> |
| 5 | 69 <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR. |
| 70 This ATLAS build includes patches from the Debian ATLAS packages which enable additional features: | |
| 71 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions | |
| 72 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories | |
| 73 This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$ATLAS_LIB_DIR so that any dependent packages which link to ATLAS will be able to resolve all necessary libraries at runtime. | |
| 74 On Mac OS X, this package is a dummy package - BLAS and LAPACK libraries are already provided in Apple's vecLib. | |
| 0 | 75 </readme> |
| 76 </package> | |
| 77 </tool_dependency> |