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 |
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src | |
| GROMOS |
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/opt/GROMOS/gromos96_24Jun04/LINUX_IFC/bin/
promd, promd_opt_omp (works for two processors will try for 8 after ice comes across) | |
| gv |
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| xemacs |
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| zsh |
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| vim |
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| lam_mpi |
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src | |
| mplayer |
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No codecs installed | |
| vlc |
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| fftw |
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src | |
| 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 |
