Software: Difference between revisions

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


  '''***''' =  HAS BEEN INSTALLED
This is a listing of the 3rd-party packages are currently installed on the workstations. This list has been compiled by Mitchell Stanton-Cook
Anything that has to be built from SRC will be added to a local yum repository on compbio
 
  Packages tagged '''From SRC rpm''' will be added to a local yum repository on compbio
  '''bold''' = newly added
  '''bold''' = newly added
 
Related: SEE - '''[[yum_repo]]''' and '''[[building_rpms]]'''
 
----
LEGEND:
[[Image:Tick.jpg|Yes]]  Have been installed/tested  [[Image:Tick_yellow.jpg|Maybe]]  Close to working  [[Image:Cross.jpg|No]]  Have not been installed/tested
[[Image:Question_mark.jpg|???]]  Need more information  [[Image:Md_todo.jpg|Todo]]  A MD Group member will need to install this




{| border="1"
{| border="1"
|-
|-
!Name
!Package name
!Installed  
!Version
!Installed
!Tested
!Notes
!Notes
|-
|'''pgi'''
|'''7.2'''
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
| SEE: /opt/pgi on guava and /software/pgi on grape
|-
|-
|'''checkinstall'''
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|See [[checkinstall_patch]]. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm
|-
|-
|'''kile'''
|'''kile'''
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|'''apbs'''
|'''apbs'''
|N
|
|From src
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|src and binary. In /opt
|-
|-
|molmol
|molmol
|N
|
|
[[Image:Cross.jpg|No]]
|
[[Image:Cross.jpg|No]]
|Will buy beer if you can get this one working
|Will buy beer if you can get this one working
|-
|-
|pymol
|pymol
|N
|
|From src
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|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'''
|'''pdfedit'''
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|emacs
|emacs
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|gnuplot
|gnuplot
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|gtk
|gtk
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|gtk-devel
|gtk-devel
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|xplor-nih
|xplor-nih
|N
|
|Binary only
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|binary only
Could not run the test-scripts ! Check !!!
|-
|-
|clustal
|clustalw and clustalx
|N
|
|From src/binary
|
[[Image:Tick_yellow.jpg|No]]
|
[[Image:Cross.jpg|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
|modeller
|N
|
|
[[Image:Cross.jpg|No]]
|
[[Image:Cross.jpg|No]]
|REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm
|REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm
|-
|-
|openGL
|openGL
|Y
|
|free-glut ???
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|is this free-glut ?
|-
|-
|rasmol
|rasmol
|N
|
|src and binary
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm
|-
|-
|seqview
|seqview
|N
|
|COULD SOMEONE PROVIDE ME A URL
|
[[Image:Question_mark.jpg|???]]
|
[[Image:Cross.jpg|No]]
|'''Need url please'''
|-
|-
|treeview
|treeview
|N
|
|src
|
[[Image:Cross.jpg|No]]
|
[[Image:Cross.jpg|No]]
|src. In /opt
Requires: wxGTK
 
Have a compilation error
|-
|-
|electric fence library
|electric fence library
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|phylip
|phylip
|N
|
|src and binary
|
[[Image:Tick_yellow.jpg|No]]
|
[[Image:Cross.jpg|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
|blast
|N
|
|BLAST and wwwblast + Human EST DB for testing
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|From binary. In /opt
No DB installed
TODO: Install wwwblast on compbio
|-
|-
|VMD
|VMD
|N
|
|src
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|From src. In /opt
I will try to create a rpm package for this.
|-
|-
|povray
|povray
|N
|
|src
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|From SRC rpm. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm
|-
|-
|mead  
|mead  
|N
|
|
[[Image:Question_mark.jpg|???]]
|
[[Image:Cross.jpg|No]]
| '''Need url please'''
| '''Need url please'''
|-
|-
|spdb
|spdb
|N
|
|Don't believe is possible - do it yourself/show me !!! See '''*'''
|
[[Image:Tick_yellow.jpg|No]]
|
[[Image:Cross.jpg|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
|rxvt
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|xterm
|xterm
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|GROMACS
|GROMACS
|N
|3.2.1
3.3.1
3.3.1-CVS
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|src
|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
|GROMOS
|N
|
|src
|
[[Image:Cross.jpg|No]]
|
[[Image:Cross.jpg|No]]
|promd, promd_opt_omp (works for two processors will try for 8 after ice comes across) &ndash; <u>''Does '''NOT''' work!</u> (so-called known problem, but not solved)''
/opt/GROMOS/gromos96_24Jun04/LINUX_IFC/bin/
|-
|'''gromos++'''
|'''0.2.4'''
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Tick.jpg|Yes]]
| Jul 2008 Forcefield files in /software/gromos/forcefield  SEE: /software/gromos/gromos++ on grape
PATH=$PATH:/software/libtool/bin
./Config.sh
export FFFLAGS=-I/software/pgi/linux86-64/7.2-2/include
export LDFLAGS=-L/usr/local/lib
./configure
make
make check
make install
|-
|'''gromosXX'''
|'''0.3.0'''
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Tick.jpg|Yes]]
| Jul 2008 Forcefield files in /software/gromos/forcefield  SEE: /software/gromos/gromosXX on grape - Documentation /software/gromos/gromosXX/doc/html/index.html
PATH=$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'''
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|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
|gv
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|xemacs
|xemacs
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|zsh
|zsh
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|vim
|vim
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|lam_mpi
|LAM/MPI
|N
|7.1.4
|src
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|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
|mplayer
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|No codecs installed
|No codecs installed
|-
|-
|vlc
|vlc
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|fftw
|fftw
|N
|2.1.5
|src
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|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
|R
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|xmms-mp3
|xmms-mp3
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|installed AUDACIOUS instead
|installed AUDACIOUS instead
|-
|-
|flash
|flash
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|shockwave
|shockwave
|?  
|
|Is this available on linux? I think flash takes care of this.
|
[[Image:Question_mark.jpg|???]]
|
[[Image:Cross.jpg|No]]
|Is this available for linux? Does flash take care of this?
|-
|-
|acrobat
|acrobat
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|xmgrace
|xmgrace
|N
|
|src
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
Requires: Motif/LessTif
yum install lesstif (note: only i386 available)
yum install grace (note: installs fftw2
|-
|-
|firefox
|firefox
| Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|thunderbird
|thunderbird
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|nedit
|nedit
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|
|-
|-
|java
|java
|Y
|
|Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON.
|-
|-
|'''xine'''
|'''xine'''
|Y
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|-
|'''wxMaxima'''
|
|[[Image:Tick.jpg|Yes]]
|
|
|-
|'''nedit'''
|
|[[Image:Tick.jpg|Yes]]
|
|
|-
|'''K3b'''
|
|[[Image:Tick.jpg|Yes]]
|
|
|-
|'''mutt'''
|
|[[Image:Tick.jpg|Yes]]
|
|
|-
|'''rxvt'''
|
|[[Image:Tick.jpg|Yes]]
|
|
|-
|'''gsl (GNU Scientific Librairy) >= 1.10'''
|
|[[Image:Tick.jpg|Yes]]
|
|
|-
|'''Anjuta <= 2.2.1'''
|
|[[Image:Tick.jpg|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
|
|
[[Image:Tick.jpg|Yes]]
|
[[Image:Cross.jpg|No]]
|
|-
|DSSP
|
|
|
|Should be install at /usr/local/bin/dssp for compatibility with GROMACS.
|-
|}
|}
===Tutorials===
GROMOS Tutorial July 2008 [[http://compbio.chemistry.uq.edu.au/mediawiki/upload/2/2f/GROMOS_tutorial.pdf]]
===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

Latest revision as of 23:58, 19 February 2009

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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