Bsoft
| Description | ||
|
Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. |
||
| Site | Version (Latest: v1.5.4) | Notes |
| ngs.rl.ac.uk | v1.5.4 | 32 & 64 bit |
License
The Bsoft software is free to use and does not need any special permissions to run on the NGS.
Running the Bsoft on the NGS (General)
There a multiple ways in which jobs can be launched on the NGS
- Submission Using UI/WMS
- NGS Web Portal Submission
- Submission Using Globus
All components of Bsoft are launched in the same way using the /usr/ngs/BSOFT or /usr/ngs/BSOFT32 'UEE' scripts as below.
- Example-run of the Bsoft bimg binary on ngs.rl.ac.uk
- stdout and stderr are set to 'bimg.stdout' and 'bimg.stderr' respectively.
- The first argument must be the program we want to run. ( bimg in this case)
- The input files must be given as argument and not as stdin .
- Replace 'ngsXXXX' by your user id on ngs.rl.ac.uk. directory Is the working directory for the job, in this case a subdirectory of your homedir called 'bsoft'
- Replace BSOFT by BSOFT32 to use the 32bit version of the Bsoft binaries in the (executable=....) RSL parameter.
To submit a bimg job to truncate the data in an image between the values 0 and 100 and with verbose output, use the following command (one line NOT including the
backslashes '\'). :globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
'&(executable=/usr/ngs/BSOFT) \
(arguments= bimg -verbose 7 -truncate 0,100 input.img output.img) \
(jobType=single)(directory=/home/ngsXXXX/bsoft) \
(stdout=bimg.stdout)(stderr=bimg.stderr)'where :
- Local Submissions
This service is coming soon
After logging in to the NGS Portal, select the "Bsoft" template under the " Image Analysis" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.
Running Bsoft binaries as part of a script on ngs.rl.ac.uk
Bsoft binaries are often used with other programs to perform a sequence of tasks in a script. For example the PFT3DR programs are often used in conjunction with Bsoft in a script. The script is then submitted to the grid rather than the individual programs one at a time.
When using Bsoft as part of a script the relevant environment module can be loaded to setup the path and other environment variables as below :
module load bsoft/64/1.5.4 To load the 64bit Bsoft binaries module load bsoft/32/1.5.4 To load the 32bit Bsoft binaries
Compilation Information for ngs.rl.ac.uk
Bsoft was compiled using gcc 3.4.6.
If you need information on how this application was compiled please contact the NGS support centre.
Further Information
Applications Support
The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.
Acknowledgements
Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.
