Software: Difference between revisions
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|src - no up-to-date binaries are provided now without a license | |src - no up-to-date binaries are provided now without a license | ||
python setup.py build | python setup.py build | ||
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[[Image:Tick.jpg|Yes]] | [[Image:Tick.jpg|Yes]] | ||
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|binary only | |binary only | ||
Could not run the test-scripts ! Check !!! | Could not run the test-scripts ! Check !!! | ||
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[[Image:Tick_yellow.jpg|No]] | [[Image:Tick_yellow.jpg|No]] | ||
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[[Image:Cross.jpg|No]] | |||
|src and binary | |src and binary | ||
NCBI-devel is needed by clustalx-1.8.3-2a.x86_64 | NCBI-devel is needed by clustalx-1.8.3-2a.x86_64 | ||
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[[Image:Cross.jpg|No]] | [[Image:Cross.jpg|No]] | ||
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[[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 | ||
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[[Image:Tick.jpg|Yes]] | [[Image:Tick.jpg|Yes]] | ||
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[[Image:Cross.jpg|No]] | |||
|is this free-glut ? | |is this free-glut ? | ||
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[[Image:Tick.jpg|Yes]] | [[Image:Tick.jpg|Yes]] | ||
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[[Image:Cross.jpg|No]] | |||
|From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm | |From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm | ||
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[[Image:Question_mark.jpg|???]] | [[Image:Question_mark.jpg|???]] | ||
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[[Image:Cross.jpg|No]] | |||
|'''Need url please''' | |'''Need url please''' | ||
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[[Image:Cross.jpg|No]] | [[Image:Cross.jpg|No]] | ||
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[[Image:Cross.jpg|No]] | |||
|src | |src | ||
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[[Image:Tick_yellow.jpg|No]] | [[Image:Tick_yellow.jpg|No]] | ||
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[[Image:Cross.jpg|No]] | |||
|src and binary. | |src and binary. | ||
EMBOSS-devel = 5.0.0 is needed by PHYLIP-3.6b-6.x86_64 | EMBOSS-devel = 5.0.0 is needed by PHYLIP-3.6b-6.x86_64 | ||
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[[Image:Tick.jpg|Yes]] | [[Image:Tick.jpg|Yes]] | ||
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[[Image:Cross.jpg|No]] | |||
|From binary. In /opt | |From binary. In /opt | ||
No DB installed | No DB installed | ||
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[[Image:Tick.jpg|Yes]] | [[Image:Tick.jpg|Yes]] | ||
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|From src. In /opt | |From src. In /opt | ||
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|From SRC rpm. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm | |From SRC rpm. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm | ||
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[[Image:Question_mark.jpg|???]] | [[Image:Question_mark.jpg|???]] | ||
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[[Image:Cross.jpg|No]] | |||
| '''Need url please''' | | '''Need url please''' | ||
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[[Image:Tick_yellow.jpg|No]] | [[Image:Tick_yellow.jpg|No]] | ||
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|Building from SRC rpm. These are the steps I carried out as I could not rebuild directly | |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 | rpm -iUvh spdbv-3.7.5-3.src.rpm | ||
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[[Image:Md_todo.jpg|Todo]] | [[Image:Md_todo.jpg|Todo]] | ||
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|src | |src | ||
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[[Image:Md_todo.jpg|Todo]] | [[Image:Md_todo.jpg|Todo]] | ||
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|src | |src | ||
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[[Image:Md_todo.jpg|Todo]] | [[Image:Md_todo.jpg|Todo]] | ||
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|src | |src | ||
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|No codecs installed | |No codecs installed | ||
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|src | |src | ||
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|installed AUDACIOUS instead | |installed AUDACIOUS instead | ||
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[[Image:Question_mark.jpg|???]] | [[Image:Question_mark.jpg|???]] | ||
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|Is this available for linux? Does flash take care of this? | |Is this available for linux? Does flash take care of this? | ||
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Requires: Motif/LessTif | Requires: Motif/LessTif | ||
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[[Image:Tick.jpg|Yes]] | [[Image:Tick.jpg|Yes]] | ||
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|nedit | |nedit | ||
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[[Image:Tick.jpg|Yes]] | [[Image:Tick.jpg|Yes]] | ||
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|Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON. | |Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON. | ||
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|} | |} |
Revision as of 09:27, 12 August 2007
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 | ||||
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 !!! | |||
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 | ||||
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 | ||||
xterm | ||||
GROMACS | src | |||
GROMOS | src | |||
gv | ||||
xemacs | ||||
zsh | ||||
vim | ||||
lam_mpi | src | |||
mplayer | No codecs installed | |||
vlc | ||||
fftw | src | |||
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 |
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