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structure
Overview
Strucure is a package for using multi-locus genotype data to investigate population structure.
Version 2.3.4 is installed on the CSF. It was compiled with gcc 4.8.2 and -msse4.2 . This is a 64 bit version and thus should be able to handle large datasets as mentioned on the Structure website.
Restrictions on use
Details of the licence, restrictions, links to licence docs etc
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/structure/2.3.4
Running the application
Please do not run Structure on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission – example 1
Make sure you have the modulefile loaded.
In the directory from which you wish to run the job make sure you have a mainparams and if required extraparams file.
Then in the same directory create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings structure
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Serial batch job submission – example 2
Make sure you have the modulefile loaded.
In the directory from which you wish to run the job make sure you have parameter files – these do not have to follow the stanard name, but you need to tell the software what you have called them using -m and -e in your submission script.
Then in the same directory create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings structure -m mymainparams -e myextraparams
where mymainparams and myextraparams are replaced with the names of your files.
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
No example available or not possible with the software.
If you have a need to run a large number of similar serial jobs please use job arrays.
Further info
- Structure website
- Structure Documentation. A copy of this PDF is also available on the CSF and can be read using evince:
evince $STRUCTURE_HOME/doc/structure_doc.pdf - A basic examples of
mainparamsandextraparamsfiles can be found in$STRUCTURE_HOME/params. - Sample Data Sets
Updates
None.