From Fedora Project Wiki
(→Bundled packages which should be fine to put in Fedora: add boost-numeric-bindings from boost sandbox (required by mtkpp)) |
(ucpp is in Fedora now) |
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| tinyxml || src/mtkpp/src/tinyxml || 2.0 (April 2005) | | tinyxml || src/mtkpp/src/tinyxml || 2.0 (April 2005) | ||
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| ucpp || src/ucpp-1.3 || 1.3 | |||
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| xblas || src/xblas || 1.0 (2005) | | xblas || src/xblas || 1.0 (2005) | ||
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! Fedora package || Upstream || Version in AmberTools || Review Request/Status | ! Fedora package || Upstream || Version in AmberTools || Review Request/Status | ||
|- | |- | ||
| boost-numeric-bindings || http://beta.boost.org/community/sandbox.html || || | | boost-numeric-bindings || http://beta.boost.org/community/sandbox.html || || (not necessary for build) | ||
|- | |- | ||
| cifparse || http://sw-tools.pdb.org/apps/CIFPARSE/source.html || || | | cifparse || http://sw-tools.pdb.org/apps/CIFPARSE/source.html || || | ||
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| mtkpp || http://mtkpp.martinpeters.ie/ || 0.2.0 || | | mtkpp || http://mtkpp.martinpeters.ie/ || 0.2.0 || | ||
|- | |- | ||
| Wcl || http://search.cpan.org/~jhpb/Wcl-2.7.3/ || || [https://bugzilla.redhat.com/show_bug.cgi?id=192417 Old review request] | | Wcl || http://search.cpan.org/~jhpb/Wcl-2.7.3/ || || [https://bugzilla.redhat.com/show_bug.cgi?id=192417 Old review request] | ||
Latest revision as of 12:52, 11 March 2014
This is to help document the process to get AmberTools, a set of tools for Assisted Model Building with Energy Refinement (AMBER) into Fedora.
Bundled packages already in Fedora
| Fedora package | location in AmberTools | bundled version |
|---|---|---|
| arpack | src/arpack | 2.1 |
| blas | src/blas | 3.0? |
| boost | src/boost-1.38.0 | 1.38.0 |
| byacc | src/byacc | 20101127 |
| eigen3 | src/mtkpp/src/eigen3b2 | 3.0b2 |
| fftw | src/fftw-3.3 | 3.3 |
| lapack | src/lapack | 3.2 |
| libXmu | src/leap/src/Xmu | 20001128 |
| libXpm | src/leap/src/Xpm | 3.4 |
| mpi4py | src/mmpbsa_py/mpi4py-1.2.2.tar.gz | 1.2.2 |
| netcdf | src/netcdf | 3.6.2b6 |
| tinyxml | src/mtkpp/src/tinyxml | 2.0 (April 2005) |
| ucpp | src/ucpp-1.3 | 1.3 |
| xblas | src/xblas | 1.0 (2005) |
Bundled packages which should be fine to put in Fedora
| Fedora package | Upstream | Version in AmberTools | Review Request/Status |
|---|---|---|---|
| boost-numeric-bindings | http://beta.boost.org/community/sandbox.html | (not necessary for build) | |
| cifparse | http://sw-tools.pdb.org/apps/CIFPARSE/source.html | ||
| libpdb | http://www.cgl.ucsf.edu/Overview/software.html | bundled in ptraj | |
| libpdb++ | http://www.cgl.ucsf.edu/Overview/software.html | bundled in reduce | |
| mtkpp | http://mtkpp.martinpeters.ie/ | 0.2.0 | |
| Wcl | http://search.cpan.org/~jhpb/Wcl-2.7.3/ | Old review request |
Bundled packages which may be problematic to put in Fedora
| Name | Upstream | Version in AmberTools | Status |
|---|---|---|---|
| chamber | AmberTools | non-free license? | |
| libXraw | http://canonical.org/~kragen/Xraw/index.html | non-commercial clause in license | |
| leap | AmberTools | non-free license? | |
| reduce | http://kinemage.biochem.duke.edu/software/reduce.php | 3.14.080821 | sale restriction? |