Software
Software that is installed or is to be installed on the workstations
Packages tagged src will be added to a local yum repository on compbio bold = newly added Related: SEE - yum_repo and building_rpms
| Package name | Version | Installed | Tested | Notes |
|---|---|---|---|---|
| checkinstall |
|
See checkinstall_patch. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm | ||
| kile |
|
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| 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 |
|
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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 |
|
binary only
Could not run the test-scripts ! Check !!! | ||
| clustal |
|
src and binary
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 | ||
| electric fence library |
|
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| phylip |
|
src and binary.
EMBOSS-devel = 5.0.0 is needed by PHYLIP-3.6b-6.x86_64 | ||
| blast |
|
From binary. In /opt
No DB installed TODO: Install wwwblast on compbio | ||
| VMD |
|
From src. In /opt | ||
| 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 | ||
| rxvt |
|
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| xterm |
|
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| GROMACS |
|
src | ||
| GROMOS |
|
src | ||
| gv |
|
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| xemacs |
|
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| zsh |
|
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| vim |
|
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| lam_mpi |
|
src | ||
| mplayer |
|
No codecs installed | ||
| vlc |
|
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| fftw |
|
src | ||
| R |
|
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| xmms-mp3 |
|
installed AUDACIOUS instead | ||
| flash |
|
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| shockwave | ? | Is this available for linux? Does flash take care of this? | ||
| acrobat |
|
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| xmgrace |
|
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 |
|
Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON. | ||
| xine |
|
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
Fedora Software Groups
- To create rpm's for the correct group
Amusements/Games
Amusements/Graphics
Applications/Archiving
Applications/Communications
Applications/Databases
Applications/Editors
Applications/Emulators
Applications/Engineering
Applications/File
Applications/Internet
Applications/Multimedia
Applications/Productivity
Applications/Publishing
Applications/System
Applications/Text
Development/Debuggers
Development/Languages
Development/Libraries
Development/System
Development/Tools
Documentation
System Environment/Base
System Environment/Daemons
System Environment/Kernel
System Environment/Libraries
System Environment/Shells
User Interface/Desktops
User Interface/X
User Interface/X Hardware Support
