Mercurial > repos > iuc > package_atlas_3_10

annotate tool_dependencies.xml @ 7:98c017ec230d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 9d1bd84fdaa259740d8f75ede9ecfce9403b253a-dirty
author iuc
date Tue, 21 Jun 2016 15:28:12 -0400
parents 9b900e1578be
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
iuc
parents: 3
diff changeset
1 <?xml version="1.0"?>
0
597c0e54eded initial upload
iuc
parents:
diff changeset
2 <tool_dependency>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
3 <package name="atlas" version="3.10.2">
0
597c0e54eded initial upload
iuc
parents:
diff changeset
4 <install version="1.0">
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
5 <actions_group>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
6 <actions architecture="x86_64" os="linux">
5
c0a66ce2a119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents: 4
diff changeset
7 <action type="download_by_url" sha256sum="c36a9edf352aa3652ae2c3cccf752351e12291c1d018da842093f9dc70fa2da3">https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz</action>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
8 <action type="move_directory_files">
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
9 <source_directory>.</source_directory>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
10 <destination_directory>$INSTALL_DIR</destination_directory>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
11 </action>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
12 <action type="set_environment">
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
13 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
14 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
15 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
16 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
4
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
iuc
parents: 3
diff changeset
17 <environment_variable action="set_to" name="ATLAS">$INSTALL_DIR</environment_variable>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
18 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
19 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
3
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
20 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
21 </action>
3
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
22 <action type="shell_command"><![CDATA[
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
23 command -v gfortran || return 0
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
24 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
25 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
26 echo 'program test; end program test' > test.f90 &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
27 gfortran -o test test.f90 &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
28 LGF=`ldd test | grep libgfortran | awk '{print $3}'` &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
29 LGF_CANON=`readlink -f $LGF` &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
30 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
31 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
32 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &&
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
33 cp -p $LGF_CANON $BUNDLED_LGF_CANON
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
34 fi
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
35 ]]></action>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
36 </actions>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
37 <actions architecture="x86_64" os="darwin">
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
38 <!-- NOOP: On OS X we will use Apple's vecLib -->
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
39 </actions>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
40 <actions>
5
c0a66ce2a119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents: 4
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>
c0a66ce2a119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents: 4
diff changeset
42 <action type="download_file" sha256sum="9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352">https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz</action>
c0a66ce2a119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents: 4
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>
c0a66ce2a119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents: 4
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>
c0a66ce2a119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents: 4
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>
4
f27d2f8761ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty
iuc
parents: 3
diff changeset
46 <action type="shell_command">tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2</action>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
47 <!-- a 64-bit architecture is assumed for compilation -->
3
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
48 <action type="shell_command"><![CDATA[
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
49 cd ATLAS &&
5
c0a66ce2a119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 4e829bc62e1328b12abf9d43112967296dcfed7a
iuc
parents: 4
diff changeset
50 mkdir build &&
6
9b900e1578be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit c2e47951d0f68e2533e45529ece8a52ab01b9cd2-dirty
iuc
parents: 5
diff changeset
51 patch -p1 < ../atlas_patch-blas-lapack-1.0_src_all.diff &&
9b900e1578be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit c2e47951d0f68e2533e45529ece8a52ab01b9cd2-dirty
iuc
parents: 5
diff changeset
52 patch -p1 < ../atlas_patch-shared-lib-1.0_src_all.diff &&
9b900e1578be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit c2e47951d0f68e2533e45529ece8a52ab01b9cd2-dirty
iuc
parents: 5
diff changeset
53 patch -p1 < ../atlas_patch-cpu-throttle-1.0_src_all.diff &&
3
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
54 cd build &&
7
98c017ec230d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 9d1bd84fdaa259740d8f75ede9ecfce9403b253a-dirty
iuc
parents: 6
diff changeset
55 ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack_3.5.0_src_all.tar.gz -v 2 -t 0 -Si cputhrchk 0 &&
3
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
56 make &&
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
57 make install
3
0538fd672119 Uploaded
iuc
parents: 2
diff changeset
58 ]]></action>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
59 <action type="set_environment">
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
60 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
61 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
62 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
63 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
64 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
65 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
2
b36c9ee883e9 Uploaded
bgruening
parents: 1
diff changeset
66 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
67 </action>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
68 </actions>
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
69 </actions_group>
0
597c0e54eded initial upload
iuc
parents:
diff changeset
70 </install>
1
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
71 <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR.
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
72 This ATLAS build includes patches from the Debian ATLAS packages which enable additional features:
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
73 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
74 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
75 This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$ATLAS_LIB_DIR so that any dependent packages which link to ATLAS will be able to resolve all necessary libraries at runtime.
37ff27ea37ed Uploaded
iuc
parents: 0
diff changeset
76 On Mac OS X, this package is a dummy package - BLAS and LAPACK libraries are already provided in Apple's vecLib.
0
597c0e54eded initial upload
iuc
parents:
diff changeset
77 </readme>
597c0e54eded initial upload
iuc
parents:
diff changeset
78 </package>
597c0e54eded initial upload
iuc
parents:
diff changeset
79 </tool_dependency>