Gemini on Biowulf
GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very powerful system for exploring genetic variation for for disease and population genetics.
References:
- Paila U, Chapman BA, Kirchner R, Quinlan AR (2013) GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. PLoS Comput Biol 9(7): e1003153. doi:10.1371/journal.pcbi.1003153
Documentation
Important Notes
- Module Name: gemini (see the modules page for more information)
- Singlethreaded
- Example files in /fdb/gemini
- Reference data in /fdb/gemini/
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ cd /data/$USER/gemini [user@cn3144 ~]$ cp -r /fdb/gemini/gemini/test . [user@cn3144 ~]$ cp /fdb/gemini/gemini/master-test.sh . [user@cn3144 ~]$ module load gemini [user@cn3144 ~]$ bash master-test.sh Bgzipping test.query.vcf into test.query.vcf.gz. Indexing test.query.vcf.gz with grabix. Loading 879 variants. Breaking test.query.vcf.gz into 2 chunks. Loading chunk 0. Loading chunk 1. Done loading 879 variants in 1 chunks. region.t01...\c ok region.t02...\c ok region.t03...\c ok region.t04...\c [...] [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. gemini.sh). For example:
#!/bin/bash cd /data/$USER/gemini cp -r /fdb/gemini/gemini/test . cp /fdb/gemini/gemini/master-test.sh . bash master-test.sh
Submit this job using the Slurm sbatch command.
sbatch --mem=5g gemini.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.