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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|is this free-glut ?
|is this free-glut ?
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[[Image:Tick.jpg|Yes]]
[[Image:Tick.jpg|Yes]]
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|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]]
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[[Image:Cross.jpg|No]]
|src
|src
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[[Image:Tick.jpg|Yes]]
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|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]]
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|From binary. In /opt
|From binary. In /opt
No DB installed
No DB installed
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|From src. In /opt
|From src. In /opt
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[[Image:Tick.jpg|Yes]]
[[Image:Tick.jpg|Yes]]
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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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| '''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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[[Image:Cross.jpg|No]]
|src
|src
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[[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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|nedit
|nedit
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[[Image:Tick.jpg|Yes]]
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[[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

Yes

No

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

Yes

No

apbs

Yes

No

src and binary. In /opt
molmol

No

No

Will buy beer if you can get this one working
pymol

Yes

No

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

No

emacs

Yes

No

gnuplot

Yes

No

gtk

Yes

No

gtk-devel

Yes

No

xplor-nih

Yes

No

binary only

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

clustal

No

No

src and binary

NCBI-devel is needed by clustalx-1.8.3-2a.x86_64

modeller

No

No

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

Yes

No

is this free-glut ?
rasmol

Yes

No

From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm
seqview

???

No

Need url please
treeview

No

No

src
electric fence library

Yes

No

phylip

No

No

src and binary.

EMBOSS-devel = 5.0.0 is needed by PHYLIP-3.6b-6.x86_64

blast

Yes

No

From binary. In /opt

No DB installed TODO: Install wwwblast on compbio

VMD

Yes

No

From src. In /opt
povray

Yes

No

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

???

No

Need url please
spdb

No

No

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

Yes

No

xterm

Yes

No

GROMACS

Todo

No

src
GROMOS

Todo

No

src
gv

Yes

No

xemacs

Yes

No

zsh

Yes

No

vim

Yes

No

lam_mpi

Todo

No

src
mplayer

Yes

No

No codecs installed
vlc

Yes

No

fftw

Todo

No

src
R

Yes

No

xmms-mp3

Yes

No

installed AUDACIOUS instead
flash

Yes

No

shockwave

???

No

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

Yes

No

xmgrace

Yes

No

Requires: Motif/LessTif 

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

Yes

No

thunderbird

Yes

No

nedit

No

Yes

java

Yes

No

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

Yes

No


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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