Software

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

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

Package name	Installation state	Notes
checkinstall	Y	See checkinstall_patch. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm
kile	Y
apbs	N	src
molmol	N	Will buy beer if you can get this one working
pymol	N	src - no up-to-date binaries are provided now without a license
pdfedit	Y
emacs	Y
gnuplot	Y
gtk	Y
gtk-devel	Y
xplor-nih	N	binary only
clustal	N	src and binary
modeller	N	REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm
openGL	Y	is this free-glut ?
rasmol	N	src and binary
seqview	N	Need url please
treeview	N	src
electric fence library	Y
phylip	N	src and binary
blast	N	BLAST and wwwblast + Human EST DB for testing
VMD	N	src
povray	Y	src. See -
mead	N	Need url please
spdb	N	Don't believe is possible - do it yourself/show me !!! See *
rxvt	Y
xterm	Y
GROMACS	N	src
GROMOS	N	src
gv	Y
xemacs	Y
zsh	Y
vim	Y
lam_mpi	N	src
mplayer	Y	No codecs installed
vlc	Y
fftw	N	src
R	Y
xmms-mp3	Y	installed AUDACIOUS instead
flash	Y
shockwave	?	Is this available for linux? Does flash take care of this?
acrobat	Y
xmgrace	N	src
firefox	Y
thunderbird	Y
nedit	Y
java	Y	Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON.
xine	Y

*I have found a few handy rpm repositories:

• • http://serine.umdnj.edu/~golharam/biorpms/downloads.php
  • http://biopackages.net/
  • http://www.biolinux.org/wiki/index.php/Main_Page
  • http://uberh4x0r.org/~yax/biorpm/
  • http://apt.bea.ki.se/
  • http://apt.bioxray.dk/rhel/el4/x86_64/html/index_xray.html

Fedora Software Groups

• To create rpm's for the correct group

Amusements/Games Amusements/Graphics Applications/Archiving Applications/Communications Applications/Databases Applications/Editors Applications/Emulators Applications/Engineering Applications/File Applications/Internet Applications/Multimedia Applications/Productivity Applications/Publishing Applications/System Applications/Text Development/Debuggers Development/Languages Development/Libraries Development/System Development/Tools Documentation System Environment/Base System Environment/Daemons System Environment/Kernel System Environment/Libraries System Environment/Shells User Interface/Desktops User Interface/X User Interface/X Hardware Support