Software: Difference between revisions

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Line 14: Line 14:
|'''checkinstall'''
|'''checkinstall'''
|
|
[[Image:Tick.jpg|This Wiki's logo]]
[[Image:Tick.jpg|Yes]]
|See [[checkinstall_patch]]. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm
|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]]
|
|
|-
|-
|'''apbs'''
|'''apbs'''
|N
|
[[Image:Cross.jpg|No]]
|src and binary.
|src and binary.
|-
|-
|molmol
|molmol
|N
|
[[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
|Y
|
[[Image:Tick.jpg|Yes]]
|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
Line 39: Line 43:
|-
|-
|'''pdfedit'''
|'''pdfedit'''
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|emacs
|emacs
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|gnuplot
|gnuplot
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|gtk
|gtk
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|gtk-devel
|gtk-devel
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|xplor-nih
|xplor-nih
|Y
|
[[Image:Tick.jpg|Yes]]
|binary only
|binary only
Could not run the test-scripts ! Check !!!
Could not run the test-scripts ! Check !!!
|-
|-
|clustal  
|clustal  
|N
|
[[Image:Cross.jpg|No]]
|src and binary
|src and binary
|-
|-
|modeller
|modeller
|N
|
[[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
|
[[Image:Tick.jpg|Yes]]
|is this free-glut ?
|is this free-glut ?
|-
|-
|rasmol
|rasmol
|N
|
[[Image:Cross.jpg|No]]
|src and binary
|src and binary
|-
|-
|seqview
|seqview
|N
|
[[Image:Cross.jpg|No]]
|'''Need url please'''
|'''Need url please'''
|-
|-
|treeview
|treeview
|N
|
[[Image:Cross.jpg|No]]
|src
|src
|-
|-
|electric fence library
|electric fence library
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
Line 96: Line 113:
|-
|-
|blast
|blast
|N
|
[[Image:Cross.jpg|No]]
|BLAST and wwwblast + Human EST DB for testing
|BLAST and wwwblast + Human EST DB for testing
|-
|-
|VMD
|VMD
|N
|
[[Image:Cross.jpg|No]]
|src
|src
|-
|-
|povray
|povray
|N
|
[[Image:Cross.jpg|No]]
|src. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm
|src. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm
|-
|-
|mead  
|mead  
|N
|
[[Image:Cross.jpg|No]]
| '''Need url please'''
| '''Need url please'''
|-
|-
|spdb
|spdb
|N
|
[[Image:Cross.jpg|No]]
|Don't believe is possible - do it yourself/show me !!! See '''*'''
|Don't believe is possible - do it yourself/show me !!! See '''*'''
OK - I have found a src rpm. These are the steps I carried out as I could not rebuild directly
OK - I have found a src rpm. These are the steps I carried out as I could not rebuild directly
Line 123: Line 145:
|-
|-
|rxvt
|rxvt
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|xterm
|xterm
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|GROMACS
|GROMACS
|N
|
[[Image:Cross.jpg|No]]
|src '''MD GROUP CAN DO THIS ONE'''
|src '''MD GROUP CAN DO THIS ONE'''
|-
|-
|GROMOS
|GROMOS
|N
|
[[Image:Cross.jpg|No]]
|src '''MD GROUP CAN DO THIS ONE'''
|src '''MD GROUP CAN DO THIS ONE'''
|-
|-
|gv
|gv
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|xemacs
|xemacs
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|zsh
|zsh
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|vim
|vim
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|lam_mpi
|lam_mpi
|N
|
[[Image:Cross.jpg|No]]
|src '''MD GROUP CAN DO THIS ONE'''
|src '''MD GROUP CAN DO THIS ONE'''
|-
|-
|mplayer
|mplayer
|Y
|
[[Image:Tick.jpg|Yes]]
|No codecs installed
|No codecs installed
|-
|-
|vlc
|vlc
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|fftw
|fftw
|N
|
[[Image:Cross.jpg|No]]
|src '''MD GROUP CAN DO THIS ONE'''
|src '''MD GROUP CAN DO THIS ONE'''
|-
|-
|R
|R
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|xmms-mp3
|xmms-mp3
|Y
|
[[Image:Tick.jpg|Yes]]
|installed AUDACIOUS instead
|installed AUDACIOUS instead
|-
|-
|flash
|flash
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
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|-
|-
|acrobat
|acrobat
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|xmgrace
|xmgrace
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
Requires: Motif/LessTif
Requires: Motif/LessTif
Line 198: Line 237:
|-
|-
|firefox
|firefox
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|thunderbird
|thunderbird
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|nedit
|nedit
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|-
|-
|java
|java
|Y
|
[[Image:Tick.jpg|Yes]]
|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.
|-
|-
|'''xine'''
|'''xine'''
|Y
|
[[Image:Tick.jpg|Yes]]
|
|
|}
|}

Revision as of 05:40, 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 Installation state Notes
checkinstall

Yes

See checkinstall_patch. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm
kile

Yes

apbs

No

src and binary.
molmol

No

Will buy beer if you can get this one working
pymol

Yes

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

emacs

Yes

gnuplot

Yes

gtk

Yes

gtk-devel

Yes

xplor-nih

Yes

binary only

Could not run the test-scripts ! Check !!!

clustal

No

src and binary
modeller

No

REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm
openGL

Yes

is this free-glut ?
rasmol

No

src and binary
seqview

No

Need url please
treeview

No

src
electric fence library

Yes

phylip N src and binary
blast

No

BLAST and wwwblast + Human EST DB for testing
VMD

No

src
povray

No

src. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm
mead

No

Need url please
spdb

No

Don't believe is possible - do it yourself/show me !!! See *

OK - I have found a 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

WE NOW HAVE: /usr/src/redhat/RPMS/x86_64/spdbv-3.7.5-3.x86_64.rpm

rxvt

Yes

xterm

Yes

GROMACS

No

src MD GROUP CAN DO THIS ONE
GROMOS

No

src MD GROUP CAN DO THIS ONE
gv

Yes

xemacs

Yes

zsh

Yes

vim

Yes

lam_mpi

No

src MD GROUP CAN DO THIS ONE
mplayer

Yes

No codecs installed
vlc

Yes

fftw

No

src MD GROUP CAN DO THIS ONE
R

Yes

xmms-mp3

Yes

installed AUDACIOUS instead
flash

Yes

shockwave ? Is this available for linux? Does flash take care of this?
acrobat

Yes

xmgrace

Yes

Requires: Motif/LessTif 

yum install lesstif (note: only i386 available)
yum install grace (note: installs fftw2
firefox

Yes

thunderbird

Yes

nedit

Yes

java

Yes

Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON.
xine

Yes


Bioinformatics/Computational Biology/X-ray Crystallography rpm repositories


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

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