AmberTools

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=== 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 || Version in AmberTools
+
! Fedora package || Upstream || Version in AmberTools || Review Request/Status
 
|-
 
|-
 
| cifparse || http://sw-tools.pdb.org/apps/CIFPARSE/source.html || ||
 
| cifparse || http://sw-tools.pdb.org/apps/CIFPARSE/source.html || ||
 
|-
 
|-
| libpdb++ || http://www.cgl.ucsf.edu/Overview/software.html || bundled in reduce ||
+
| libpdb || http://www.cgl.ucsf.edu/Overview/software.html || || bundled in ptraj
 
|-
 
|-
| mtkpp || http://mtkpp.martinpeters.ie/ || || 0.2.0
+
| libpdb++ || http://www.cgl.ucsf.edu/Overview/software.html || || bundled in reduce
 
|-
 
|-
| ucpp || http://code.google.com/p/ucpp/ || || 1.3
+
| 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] ||
+
| ucpp || http://code.google.com/p/ucpp/ || 1.3 ||
 +
|-
 +
| Wcl || http://search.cpan.org/~jhpb/Wcl-2.7.3/ || || [https://bugzilla.redhat.com/show_bug.cgi?id=192417 Old review request]
 
|}
 
|}
  

Revision as of 21:25, 11 May 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
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)
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
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
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 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?