Mercurial > repos > iuc > package_atlas_3_10
annotate tool_dependencies.xml @ 9:35d6b30ef137 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
| author | iuc |
|---|---|
| date | Thu, 16 Jun 2016 12:13:45 -0400 |
| parents | c47756a8136e |
| children |
| rev | line source |
|---|---|
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c47756a8136e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
iuc
parents:
7
diff
changeset
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1 <?xml version="1.0"?> |
| 0 | 2 <tool_dependency> |
| 5 | 3 <package name="atlas" version="3.10.2"> |
| 0 | 4 <install version="1.0"> |
| 5 | 5 <actions_group> |
| 6 <actions architecture="x86_64" os="linux"> | |
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9
35d6b30ef137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents:
8
diff
changeset
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7 <action type="download_by_url" sha256sum="c36a9edf352aa3652ae2c3cccf752351e12291c1d018da842093f9dc70fa2da3">https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz</action> |
| 5 | 8 <action type="move_directory_files"> |
| 9 <source_directory>.</source_directory> | |
| 10 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 11 </action> | |
| 12 <action type="set_environment"> | |
| 13 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> | |
| 14 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> | |
| 15 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
| 16 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
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8
c47756a8136e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
iuc
parents:
7
diff
changeset
|
17 <environment_variable action="set_to" name="ATLAS">$INSTALL_DIR</environment_variable> |
| 5 | 18 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> |
| 19 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> | |
| 7 | 20 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable> |
| 5 | 21 </action> |
| 7 | 22 <action type="shell_command"><![CDATA[ |
| 23 command -v gfortran || return 0 | |
| 24 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 && | |
| 25 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && | |
| 26 echo 'program test; end program test' > test.f90 && | |
| 27 gfortran -o test test.f90 && | |
| 28 LGF=`ldd test | grep libgfortran | awk '{print $3}'` && | |
| 29 LGF_CANON=`readlink -f $LGF` && | |
| 30 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && | |
| 31 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then | |
| 32 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled && | |
| 33 cp -p $LGF_CANON $BUNDLED_LGF_CANON | |
| 34 fi | |
| 35 ]]></action> | |
| 5 | 36 </actions> |
| 37 <actions architecture="x86_64" os="darwin"> | |
| 38 <!-- NOOP: On OS X we will use Apple's vecLib --> | |
| 39 </actions> | |
| 40 <actions> | |
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9
35d6b30ef137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents:
8
diff
changeset
|
41 <action type="download_file" sha256sum="3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f">https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2</action> |
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35d6b30ef137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents:
8
diff
changeset
|
42 <action type="download_file" sha256sum="9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352">https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz</action> |
|
35d6b30ef137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents:
8
diff
changeset
|
43 <action type="download_file" sha256sum="adbe462b179a2d626cd229cddcb08e39ae2f2544eccf80ab617790b307667146">https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff</action> |
|
35d6b30ef137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents:
8
diff
changeset
|
44 <action type="download_file" sha256sum="95862478f7d276f948a58c583acd2935ada9ad3bb55944a303d94e161e202d89">https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff</action> |
|
35d6b30ef137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents:
8
diff
changeset
|
45 <action type="download_file" sha256sum="f805600c46719f74752e9026e1461d084a385ba67838364a81c36cdfb69cad82">https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff</action> |
|
8
c47756a8136e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
iuc
parents:
7
diff
changeset
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46 <action type="shell_command">tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2</action> |
| 5 | 47 <!-- a 64-bit architecture is assumed for compilation --> |
| 7 | 48 <action type="shell_command"><![CDATA[ |
| 49 cd ATLAS && | |
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35d6b30ef137
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents:
8
diff
changeset
|
50 mkdir build && |
| 7 | 51 patch -p1 </host/static_full_blas_lapack.diff && |
| 52 patch -p1 </host/shared_libraries.diff && | |
| 53 patch -p1 </host/cpu-throttling-check.diff && | |
| 54 cd build && | |
| 55 ../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 && | |
| 56 make && | |
| 5 | 57 make install |
| 7 | 58 ]]></action> |
| 5 | 59 <action type="set_environment"> |
| 60 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> | |
| 61 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> | |
| 62 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
| 63 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> | |
| 64 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 65 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> | |
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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
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66 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable> |
| 5 | 67 </action> |
| 68 </actions> | |
| 69 </actions_group> | |
| 0 | 70 </install> |
| 5 | 71 <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR. |
| 72 This ATLAS build includes patches from the Debian ATLAS packages which enable additional features: | |
| 73 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions | |
| 74 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories | |
| 75 This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$ATLAS_LIB_DIR so that any dependent packages which link to ATLAS will be able to resolve all necessary libraries at runtime. | |
| 76 On Mac OS X, this package is a dummy package - BLAS and LAPACK libraries are already provided in Apple's vecLib. | |
| 0 | 77 </readme> |
| 78 </package> | |
| 79 </tool_dependency> |