AmberTools

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=== Bundled packages already in Fedora ===
 
=== Bundled packages already in Fedora ===
 
{|
 
{|
! Fedora package || Version in AmberTools
+
! 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
 
|-
 
|-
| eigen || 2.92
+
| eigen || 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)
+
| xblas || src/xblas || 1.0 (2005)
 
|}
 
|}
  

Revision as of 19:43, 9 April 2013

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
eigen 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)
xblas src/xblas 1.0 (2005)

Bundled packages which should be fine to put in Fedora

Fedora package Upstream Review Request/Status Version in AmberTools
cifparse http://sw-tools.pdb.org/apps/CIFPARSE/source.html
libpdb++ http://www.cgl.ucsf.edu/Overview/software.html bundled in reduce
mtkpp http://mtkpp.martinpeters.ie/ 0.2.0
ucpp http://code.google.com/p/ucpp/ 1.3
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 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 sale restriction?