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comparison tool_dependencies.xml @ 5:c0a66ce2a119 draft

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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 12:14:27 -0400
parents f27d2f8761ae
children 9b900e1578be
comparison
equal deleted inserted replaced
4:f27d2f8761ae 5:c0a66ce2a119
2 <tool_dependency> 2 <tool_dependency>
3 <package name="atlas" version="3.10.2"> 3 <package name="atlas" version="3.10.2">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions_group> 5 <actions_group>
6 <actions architecture="x86_64" os="linux"> 6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url" sha256sum="c36a9edf352aa3652ae2c3cccf752351e12291c1d018da842093f9dc70fa2da3"> 7 <action type="download_by_url" sha256sum="c36a9edf352aa3652ae2c3cccf752351e12291c1d018da842093f9dc70fa2da3">https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz</action>
8 https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz
9 </action>
10 <action type="move_directory_files"> 8 <action type="move_directory_files">
11 <source_directory>.</source_directory> 9 <source_directory>.</source_directory>
12 <destination_directory>$INSTALL_DIR</destination_directory> 10 <destination_directory>$INSTALL_DIR</destination_directory>
13 </action> 11 </action>
14 <action type="set_environment"> 12 <action type="set_environment">
38 </actions> 36 </actions>
39 <actions architecture="x86_64" os="darwin"> 37 <actions architecture="x86_64" os="darwin">
40 <!-- NOOP: On OS X we will use Apple's vecLib --> 38 <!-- NOOP: On OS X we will use Apple's vecLib -->
41 </actions> 39 </actions>
42 <actions> 40 <actions>
43 <action type="download_file" sha256sum="3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f"> 41 <action type="download_file" sha256sum="3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f">https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2</action>
44 https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2 42 <action type="download_file" sha256sum="9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352">https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz</action>
45 </action> 43 <action type="download_file" sha256sum="adbe462b179a2d626cd229cddcb08e39ae2f2544eccf80ab617790b307667146">https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff</action>
46 <action type="download_file" sha256sum="9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352"> 44 <action type="download_file" sha256sum="95862478f7d276f948a58c583acd2935ada9ad3bb55944a303d94e161e202d89">https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff</action>
47 https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz 45 <action type="download_file" sha256sum="f805600c46719f74752e9026e1461d084a385ba67838364a81c36cdfb69cad82">https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff</action>
48 </action>
49 <action type="download_file" sha256sum="adbe462b179a2d626cd229cddcb08e39ae2f2544eccf80ab617790b307667146">
50 https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff
51 </action>
52 <action type="download_file" sha256sum="95862478f7d276f948a58c583acd2935ada9ad3bb55944a303d94e161e202d89">
53 https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff
54 </action>
55 <action type="download_file" sha256sum="f805600c46719f74752e9026e1461d084a385ba67838364a81c36cdfb69cad82">
56 https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff
57 </action>
58 <action type="shell_command">tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2</action> 46 <action type="shell_command">tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2</action>
59 <!-- a 64-bit architecture is assumed for compilation --> 47 <!-- a 64-bit architecture is assumed for compilation -->
60 <action type="shell_command"><![CDATA[ 48 <action type="shell_command"><![CDATA[
61 cd ATLAS && 49 cd ATLAS &&
62 mkdir ATLAS/build && 50 mkdir build &&
63 patch -p1 </host/static_full_blas_lapack.diff && 51 patch -p1 </host/static_full_blas_lapack.diff &&
64 patch -p1 </host/shared_libraries.diff && 52 patch -p1 </host/shared_libraries.diff &&
65 patch -p1 </host/cpu-throttling-check.diff && 53 patch -p1 </host/cpu-throttling-check.diff &&
66 cd build && 54 cd build &&
67 ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 && 55 ../configure --prefix="$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 &&