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 |
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See checkinstall_patch. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm | |
| kile |
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| apbs |
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src and binary. In /opt | |
| molmol |
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Will buy beer if you can get this one working | |
| pymol |
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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 |
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| emacs |
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| gnuplot |
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| gtk |
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| gtk-devel |
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| xplor-nih |
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binary only
Could not run the test-scripts ! Check !!! | |
| clustalw and clustalx |
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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 |
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REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm | |
| openGL |
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is this free-glut ? | |
| rasmol |
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From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm | |
| seqview |
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Need url please | |
| treeview |
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src. In /opt
Requires: wxGTK Have a compilation error | |
| electric fence library |
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| phylip |
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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 |
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From binary. In /opt
No DB installed TODO: Install wwwblast on compbio | |
| VMD |
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From src. In /opt
I will try to create a rpm package for this. | |
| povray |
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From SRC rpm. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm | |
| mead |
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Need url please | |
| spdb |
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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 |
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| xterm |
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| GROMACS | 3.2.1
3.3.1 3.3.1-CVS |
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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 |
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promd, promd_opt_omp (works for two processors will try for 8 after ice comes across)
/opt/GROMOS/gromos96_24Jun04/LINUX_IFC/bin/ | |
| gv |
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| xemacs |
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| zsh |
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| vim |
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| LAM/MPI | 7.1.4 |
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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 |
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No codecs installed | |
| vlc |
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| fftw | 2.1.5 |
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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 |
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| xmms-mp3 |
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installed AUDACIOUS instead | |
| flash |
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| shockwave |
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Is this available for linux? Does flash take care of this? | |
| acrobat |
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| xmgrace |
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Requires: Motif/LessTif yum install lesstif (note: only i386 available) yum install grace (note: installs fftw2 | |
| firefox |
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| thunderbird |
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| nedit |
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| java |
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Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON. | |
| xine |
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| wxMaxima | 
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| nedit |
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| K3b |
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| mutt |
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| rxvt |
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| gsl (GNU Scientific Librairy) >= 1.10 |
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| Anjuta <= 2.2.1 |
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| Anjuta >= 2.2.1 :) | ||||
| compat-libf2c |
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