Software

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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
pgi 7.2

Yes

No

SEE: /opt/pgi on guava and /software/pgi on grape
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 3.2.1

3.3.1 3.3.1-CVS

Yes

No

src

3.2.1: in /opt/GROMACS/3.2.1 (All-static fails) [single and doule precision (_d)] 

./configure --prefix=/opt/GROMACS/3.2.1 --with-fft=fft F77=/opt/intel/fce/10.0.023/bin/ifort CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib [--disable-float --program-suffix=_d]
(then make and make install)

And an MPI version for mdrun (_mpi and _mpi_d) 

./configure --prefix=/opt/GROMACS/3.2.1 --with-fft=fft F77=/opt/lam-mpi-7.1.4/bin/mpif77 CC=/opt/lam-mpi-7.1.4/bin/mpicc CXX=/opt/lam-mpi-7.1.4/bin/mpiCC CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib --enable-mpi --program-suffix=_mpi [--disable-float --program-suffix=_mpi_d]

3.3.1: in /opt/GROMACS/3.3.1 (All-static fails) [single and doule precision (_d)] 

./configure --prefix=/opt/GROMACS/3.3.1 --with-fft=fftw2 F77=/opt/intel/fce/10.0.023/bin/ifort CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib [--disable-float --program-suffix=_d]

And an MPI version for mdrun (_mpi and _mpi_d) 

./configure --prefix=/opt/GROMACS/3.3.1 --with-fft=fftw2 F77=/opt/lam-mpi-7.1.4/bin/mpif77 CC=/opt/lam-mpi-7.1.4/bin/mpicc CXX=/opt/lam-mpi-7.1.4/bin/mpiCC CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib --enable-mpi --program-suffix=_mpi [--disable-float --program-suffix=_mpi_d]

3.3.1 (CVS): in /opt/GROMACS/3.3.1-CVS [single and doule precision, MPI-enabled mdrun] 

./bootstrap and then, same commands as 3.3.1
GROMOS

No

No

promd, promd_opt_omp (works for two processors will try for 8 after ice comes across) – Does NOT work! (so-called known problem, but not solved) 
/opt/GROMOS/gromos96_24Jun04/LINUX_IFC/bin/
gromos++ 0.2.4

Yes

Yes

Jul 2008 Forcefield files in /software/gromos/forcefield SEE: /software/gromos/gromos++ on grape 
PATH=$PATH:/software/libtool/bin
./Config.sh
export FFFLAGS=-I/software/pgi/linux86-64/7.2-2/include
export LDFLAGS=-L/usr/local/lib
./configure 
make
make check
make install
gromosXX 0.3.0

Yes

Yes

Jul 2008 Forcefield files in /software/gromos/forcefield SEE: /software/gromos/gromosXX on grape - Documentation /software/gromos/gromosXX/doc/html/index.html 
PATH=$PATH:/software/libtool/bin
./Config.sh
./configure --prefix=/software/gromos/gromosXX 
make
make check
make install
-for documentation-
touch doc/doxygen.conf.in
make doc
gromos96 24Jun04

Yes

No

Jul 2008 Forcefield files in /software/gromos/forcefield SEE: /software/gromos/gromos96_24Jun04 - compiled with pgf95 on GRAPE /software/gromos/gromos96_24Jun04/LINUX_PGF/bin 
make gromos
gv

Yes

No

xemacs

Yes

No

zsh

Yes

No

vim

Yes

No

LAM/MPI 7.1.4

Yes

No

src - 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

Yes

No

No codecs installed
vlc

Yes

No

fftw 2.1.5

Yes

No

src - 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

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

wxMaxima Yes
nedit Yes
K3b Yes
mutt Yes
rxvt Yes
gsl (GNU Scientific Librairy) >= 1.10 Yes
Anjuta <= 2.2.1 Yes
glade-3 >= 3.0.2 (install before anjuta) Ask me help when you install it cause there is some tricks
g77 GNU FORTRAN77 compiler
Anjuta >= 2.2.2 :) Ask me help when you install it cause there is some tricks
compat-libf2c

Yes

No

DSSP Should be install at /usr/local/bin/dssp for compatibility with GROMACS.


Tutorials

GROMOS Tutorial July 2008 [[1]]

Bioinformatics/Computational Biology/X-ray Crystallography rpm repositories

List of missing packages on CentOS workstation

Please list the ones that interest you.

Roy: AdobeReader_enu cmake gnupg2 gv maxima numpy octave rasmol scipy urlview

Thomas: The once Roy wants, the following list + all the once I forgot or didn't recognise 

      clustalw
      cracklib-python
      numpy
      pygsl
      python-biopython
      python-exif
      python-libs
      python-paste
      ScientificPython
      ScientificPython-doc
      scipy
      esound-libs
      ffmpeg-libs
      fftw2
      gsl-devel
      gtk+extra
      java-1.5.0-gcj
      java-1.5.0-gcj-devel
      java-1.5.0-gcj-javadoc
      jython
      lame-libs
      modeller
      octave
      perl-bioperl
      perl-bioperl-run
      perl-CPAN
      perl-devel
      perl-Error
      perl-ExtUtils-Embed
      perl-ExtUtils-MakeMaker
      perl-libs
      picasa
      povray
      R
      rasmol
      xemacs
      xemacs-common
      xemacs-packages-base
      xemacs-packages-extra
      xmms-libs

Mitch: AdobeReader_enu numpy octave octave-forge python-biopython R ScientificPython scigraphica scipy

HERE STARTS THE List of missing packages on CentOS workstation

       AdobeReader_enu
       adobe-release-i386
       akode
       akode-pulseaudio
       amarok
       atlas
       audacious-plugins
       audacious-plugins-nonfree-aac
       audacious-plugins-nonfree-alac
       audacious-plugins-nonfree-lame
       audacious-plugins-nonfree-mms
       audacious-plugins-nonfree-mp3
       audacious-plugins-nonfree-tta
       audacious-plugins-nonfree-wma
       autogen
       autogen-libopts
       autorun
       avahi-sharp
       BackupPC
       banshee
       blender
       Canna-libs
       checkinstall
       clustalw
       cmake
       compat-wxGTK26
       ConsoleKit
       ConsoleKit-libs
       ConsoleKit-x11
       cracklib-python
       dbus-qt
       ddd
       device-mapper-libs
       dhcpv6_client
       digikam
       dirac-libs
       dirmngr
       eclipse-cdt
       eclipse-pydev
       eclipse-subclipse
       esound-libs
       fast-user-switch-applet
       fedora-bookmarks
       fedora-logos
       fedora-release
       fedora-release-notes
       festival-lib
       festival-speechtools-libs
       festvox-ked-diphone
       festvox-slt-arctic-hts
       ffmpeg-libs
       fftw2
       file-libs
       firefox-devel
       flash-plugin
       freealut
       f-spot
       fuse-libs
       ganymed-ssh2
       gc
       GConf2-gtk
       gecko-mediaplayer
       genisoimage
       ginac
       glew
       glew-devel
       gmime-sharp
       gnome-mplayer
       gnome-sharp
       gnupg2
       gpg-pubkey
       gsl-devel
       gtk+extra
       gtkpod
       gtk-recordmydesktop
       gtk-sharp2
       gutenprint
       gutenprint-foomatic
       gutenprint-plugin
       gv
       hal-info
       hal-libs
       hunspell
       hunspell-en
       icedax
       insight
       intel-iforte100023
       intel-iforte100025
       intel-iidbe100023
       intel-iidbe100025
       istanbul
       jack-audio-connection-kit
       jack-audio-connection-kit-example-clients
       jakarta-commons-dbcp-tomcat5
       jakarta-commons-pool-tomcat5
       jasper
       java-1.5.0-gcj
       java-1.5.0-gcj-devel
       java-1.5.0-gcj-javadoc
       jython
       k3b-extras-nonfree
       kdebindings-dcopperl
       kde-filesystem
       kdegraphics-extras
       kdemultimedia-extras
       kde-settings
       kde-settings-kdm
       kdeutils-extras
       kipi-plugins
       kmod-nvidia
       knetworkmanager
       konversation
       kpowersave
       krbafs
       krbafs-devel
       lame-libs
       libbeagle
       libbinio
       libdap
       libedit
       libfreebob
       libgdiplus
       libgnomekbd
       libifp
       libipoddevice
       libiptcdata
       libkdcraw
       libkexiv2
       libkipi
       libmal
       libmtp
       libnc-dap
       libnjb
       libofa
       libopenraw
       libopenraw-gnome
       libopensync
       libreadline-java
       libscigraphica
       libsmbclient
       libsmbios-libs
       libthai
       libtiff-static
       libtirpc
       libtunepimp
       libxcb
       linuxwacom-devel
       livna-config-display
       livna-release
       maxima
       maxima-runtime-sbcl
       mcs-libs
       modeller
       mono-core
       mono-data
       mono-data-sqlite
       mono-web
       mono-winforms
       mplayer-gui
       msttcorefonts
       mysql-connector-java
       mysql-libs
       nas
       NetworkManager-openvpn
       NetworkManager-vpnc
       neXtaw
       nspluginwrapper-i386
       ntfs-3g
       numpy
       octave
       octave-forge
       openoffice.org-langpack-en
       paps-libs
       perl-bioperl
       perl-bioperl-run
       perl-CPAN
       perl-devel
       perl-Error
       perl-ExtUtils-Embed
       perl-ExtUtils-MakeMaker
       perl-libs
       picasa
       pinentry-qt
       poppler-qt
       povray
       pulseaudio-lib
       pygsl
       python-biopython
       python-exif
       python-libs
       python-paste
       qhull
       qt4-x11
       R
       radeontool
       rasmol
       RealPlayer
       recordmydesktop
       redhat-artwork-kde
       rpcbind
       sbcl
       ScientificPython
       ScientificPython-doc
       scigraphica
       scipy
       sinjdoc
       skype
       smolt
       smolt-firstboot
       spambayes
       speedcrunch
       svnkit
       tcp_wrappers-libs
       tomboy
       totem-plparser
       twolame-libs
       ufsparse
       urlview
       vbetool
       vlc-core
       VMware-server
       vnc-libs
       wavpack
       wise2
       wodim
       wxBase
       wxMaxima
       xchat-gnome
       xdg-user-dirs-gtk
       xdg-utils
       xemacs
       xemacs-common
       xemacs-packages-base
       xemacs-packages-extra
       xine-lib-extras-nonfree
       xmlrpc-c
       xmms-libs
       xorg-x11-docs
       xorg-x11-drv-apm
       xorg-x11-drv-ark
       xorg-x11-drv-chips
       xorg-x11-drv-glint
       xorg-x11-drv-i128
       xorg-x11-drv-i740
       xorg-x11-drv-nouveau
       xorg-x11-drv-nvidia
       xorg-x11-drv-nvidia-libs
       xorg-x11-drv-rendition
       xorg-x11-drv-tseng
       xorg-x11-drv-v4l
       xorg-x11-xdm
       yum-cron
       yumex
       zd1211-firmware
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