From Fedora Project Wiki

(→‎Bundled packages already in Fedora: add bundled sources location)
(ucpp is in Fedora now)
 
(6 intermediate revisions by the same user not shown)
Line 13: Line 13:
| byacc || src/byacc || 20101127
| byacc || src/byacc || 20101127
|-
|-
| eigen || src/mtkpp/src/eigen3b2 || 3.0b2
| eigen3 || src/mtkpp/src/eigen3b2 || 3.0b2
|-
|-
| fftw || src/fftw-3.3 || 3.3
| fftw || src/fftw-3.3 || 3.3
Line 28: Line 28:
|-
|-
| tinyxml || src/mtkpp/src/tinyxml || 2.0 (April 2005)
| tinyxml || src/mtkpp/src/tinyxml || 2.0 (April 2005)
|-
| ucpp || src/ucpp-1.3 || 1.3
|-
|-
| xblas || src/xblas || 1.0 (2005)
| xblas || src/xblas || 1.0 (2005)
Line 34: Line 36:
=== 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
|-
| 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++ || 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] ||
| 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?