From Fedora Project Wiki
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=== Bundled packages already in Fedora === | === Bundled packages already in Fedora === | ||
{| | {| | ||
! Fedora package || | ! Fedora package || location in AmberTools || bundled version | ||
|- | |- | ||
| arpack || 2.1 | | arpack || src/arpack || 2.1 | ||
|- | |- | ||
| blas || 3.0? | | blas || src/blas || 3.0? | ||
|- | |- | ||
| boost || 1.38 | | boost || src/boost-1.38.0 || 1.38.0 | ||
|- | |- | ||
| byacc || 20101127 | | byacc || src/byacc || 20101127 | ||
|- | |- | ||
| | | eigen3 || src/mtkpp/src/eigen3b2 || 3.0b2 | ||
|- | |- | ||
| fftw || 3.3 | | fftw || src/fftw-3.3 || 3.3 | ||
|- | |- | ||
| lapack || 3.2 | | lapack || src/lapack || 3.2 | ||
|- | |- | ||
| libXmu || 20001128 | | libXmu || src/leap/src/Xmu || 20001128 | ||
|- | |- | ||
| libXpm || 3.4 | | libXpm || src/leap/src/Xpm || 3.4 | ||
|- | |- | ||
| mpi4py || 1.2.2 | | mpi4py || src/mmpbsa_py/mpi4py-1.2.2.tar.gz || 1.2.2 | ||
|- | |- | ||
| netcdf || 3.6.2b6 | | netcdf || src/netcdf || 3.6.2b6 | ||
|- | |- | ||
| tinyxml || April 2005 | | tinyxml || src/mtkpp/src/tinyxml || 2.0 (April 2005) | ||
|- | |- | ||
| xblas || 1.0 (2005) | | ucpp || src/ucpp-1.3 || 1.3 | ||
|- | |||
| xblas || src/xblas || 1.0 (2005) | |||
|} | |} | ||
=== Bundled packages which should be fine to put in Fedora === | === Bundled packages which should be fine to put in Fedora === | ||
{| | {| | ||
! Fedora package || Upstream || Review Request/Status || | ! 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 || || | | cifparse || http://sw-tools.pdb.org/apps/CIFPARSE/source.html || || | ||
|- | |- | ||
| libpdb | | 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/ || [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] | ||
|} | |} | ||
=== Bundled packages which may be problematic to put in Fedora === | === Bundled packages which may be problematic to put in Fedora === | ||
{| | {| | ||
! Name || Upstream || Status | ! Name || Upstream || Version in AmberTools || Status | ||
|- | |- | ||
| chamber || AmberTools || non-free license? | | chamber || AmberTools || || non-free license? | ||
|- | |- | ||
| libXraw || http://canonical.org/~kragen/Xraw/index.html || non-commercial clause in license | | libXraw || http://canonical.org/~kragen/Xraw/index.html || || non-commercial clause in license | ||
|- | |- | ||
| leap || AmberTools || non-free license? | | leap || AmberTools || || non-free license? | ||
|- | |- | ||
| reduce || http://kinemage.biochem.duke.edu/software/reduce.php || sale restriction? | | reduce || http://kinemage.biochem.duke.edu/software/reduce.php || 3.14.080821 || sale restriction? | ||
|} | |} | ||
[[Category:SciTech_SIG|AmberTools]] | [[Category:SciTech_SIG|AmberTools]] | ||
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? |