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
pgi	7.2			SEE: /opt/pgi on guava and /software/pgi on grape
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	3.2.1 3.3.1 3.3.1-CVS			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				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			Jul 2008 Forcefield files in /software/gromos/forcefield SEE: /software/gromos/gromos++ on grape PATH=$PATH:/software/libtool/bin ./Config.sh export FFFLAGS=-I/software/pgi/linux86-64/7.2-2/include export LDFLAGS=-L/usr/local/lib ./configure make make check make install
gromosXX	0.3.0			Jul 2008 Forcefield files in /software/gromos/forcefield SEE: /software/gromos/gromosXX on grape - Documentation /software/gromos/gromosXX/doc/html/index.html PATH=$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			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
xemacs
zsh
vim
LAM/MPI	7.1.4			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				No codecs installed
vlc
fftw	2.1.5			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
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
K3b
mutt
rxvt
gsl (GNU Scientific Librairy) >= 1.10
Anjuta <= 2.2.1
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
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

• 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

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