Software

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:
   Have been installed/tested      Close to working      Have not been installed/tested

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

Package name	Version	Installed	Tested	Notes
checkinstall				See checkinstall_patch. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm
kile
apbs				src and binary. In /opt
molmol				Will buy beer if you can get this one working
pymol				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
emacs
gnuplot
gtk
gtk-devel
xplor-nih				binary only Could not run the test-scripts ! Check !!!
clustalw and clustalx				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				REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm
openGL				is this free-glut ?
rasmol				From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm
seqview				Need url please
treeview				src. In /opt Requires: wxGTK Have a compilation error
electric fence library
phylip				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				From binary. In /opt No DB installed TODO: Install wwwblast on compbio
VMD				From src. In /opt I will try to create a rpm package for this.
povray				From SRC rpm. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm
mead				Need url please
spdb				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
xterm
GROMACS				src
GROMOS				promd, promd_opt_omp (works for two processors will try for 8 after ice comes across) /opt/GROMOS/gromos96_24Jun04/LINUX_IFC/bin/
gv
xemacs
zsh
vim
LAM/MPI				Installed version 7.1.4. Default settings used (Fortran compiler is Intel ifort /opt/intel/fce/10.0.023/bin/ifort) ./configure --prefix=/opt/lam-mpi-7.1.4 FC=/opt/intel/fce/10.0.023/bin/ifort
mplayer				No codecs installed
vlc
fftw				Installed version 2.1.5 (single and double precision). I can't manage to install 3.0.1. ./configure --prefix=/opt/FFTW/2.1.5 --enable-mpi --enable-fortran --enable-threads --enable-type-prefix F77=/opt/lam-mpi-7.1.4/bin/mpif77 CC=/opt/lam-mpi-7.1.4/bin/mpicc FFLAGS=-L/opt/lam-mpi-7.1.4/lib/ CPPFLAGS=-I/opt/lam-mpi-7.1.4/bin [--enable-float]
R
xmms-mp3				installed AUDACIOUS instead
flash
shockwave				Is this available for linux? Does flash take care of this?
acrobat
xmgrace				Requires: Motif/LessTif yum install lesstif (note: only i386 available) yum install grace (note: installs fftw2
firefox
thunderbird
nedit
java				Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON.
xine
wxMaxima
nedit					-	rxvt

Bioinformatics/Computational Biology/X-ray Crystallography 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