Software

From MDWiki
Revision as of 11:45, 12 August 2007 by Mscook (talk | contribs)
Jump to navigationJump to search

Software that is installed or is to be installed on the workstations

This is a listing of the 3rd-party packages are currently installed on the workstations. This list has been compiled by Mitchell Stanton-Cook

Packages tagged From SRC rpm will be added to a local yum repository on compbio
bold = newly added
Related: SEE - yum_repo and building_rpms

LEGEND:
Yes   Have been installed/tested   Maybe   Close to working   No   Have not been installed/tested

???   Need more information   Todo   A MD Group member will need to install this


Package name Version Installed Tested Notes
checkinstall

Yes

No

See checkinstall_patch. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm
kile

Yes

No

apbs

Yes

No

src and binary. In /opt
molmol

No

No

Will buy beer if you can get this one working
pymol

Yes

No

src - no up-to-date binaries are provided now without a license
python setup.py build
python setup.py install
python setup2.py install
python setup2.py uninstall
cp ./pymol /usr/local/bin
pdfedit

Yes

No

emacs

Yes

No

gnuplot

Yes

No

gtk

Yes

No

gtk-devel

Yes

No

xplor-nih

Yes

No

binary only

Could not run the test-scripts ! Check !!!

clustalw and clustalx

No

No

Clustalw(INSTALLED): From SRC rpm

/usr/src/redhat/RPMS/x86_64/clustalw-1.83-0.fdr.5.x86_64.rpm

Clustalx: From SRC rpm NCBI-devel is needed by clustalx-1.8.3-2a.x86_64

modeller

No

No

REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm
openGL

Yes

No

is this free-glut ?
rasmol

Yes

No

From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm
seqview

???

No

Need url please
treeview

No

No

src. In /opt

Requires: wxGTK

Have a compilation error

electric fence library

Yes

No

phylip

No

No

Tried building from SRC rpm.

BUT, EMBOSS-devel = 5.0.0 is needed by PHYLIP-3.6b-6.x86_64

I have built from pure src. in /opt. Have not make links to /usr/local/bin

blast

Yes

No

From binary. In /opt

No DB installed TODO: Install wwwblast on compbio

VMD

Yes

No

From src. In /opt

I will try to create a rpm package for this.

povray

Yes

No

From SRC rpm. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm
mead

???

No

Need url please
spdb

No

No

Building from SRC rpm. These are the steps I carried out as I could not rebuild directly
rpm -iUvh spdbv-3.7.5-3.src.rpm
vi /usr/src/redhat/SPECS/spdbv.spec
replace Copyright with License
rpmbuild -ba /usr/src/redhat/SPECS/spdbv.spec

/usr/src/redhat/RPMS/x86_64/spdbv-3.7.5-3.x86_64.rpm

libXm.so.3 is needed by spdbv-3.7.5-3.x86_64 - This is provided by OpenMotif?

rxvt

Yes

No

xterm

Yes

No

GROMACS

Todo

No

src
GROMOS

Todo

No

src
gv

Yes

No

xemacs

Yes

No

zsh

Yes

No

vim

Yes

No

lam_mpi

Todo

No

src
mplayer

Yes

No

No codecs installed
vlc

Yes

No

fftw

Todo

No

src
R

Yes

No

xmms-mp3

Yes

No

installed AUDACIOUS instead
flash

Yes

No

shockwave

???

No

Is this available for linux? Does flash take care of this?
acrobat

Yes

No

xmgrace

Yes

No

Requires: Motif/LessTif

yum install lesstif (note: only i386 available)
yum install grace (note: installs fftw2
firefox

Yes

No

thunderbird

Yes

No

nedit

Yes

No

java

Yes

No

Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON.
xine

Yes

No


Bioinformatics/Computational Biology/X-ray Crystallography rpm repositories