example with EPACTS

epacts_slurm.sh

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+#!/bin/bash
+
+# This example demonstrates how to use SLURM with EPACTS.
+# We assume that: 
+#    (a) genotype data is saved in VCF files split by chromosome (1.vcf.gz, 2.vcf.gz and so on);
+#    (b) kinship matrix was already pre-computedi.
+
+# By default, EPACTS splits your genotypes into chunks and generates single Makefile with association test instructions for each chunk.
+# Then, EPACTS executes Makefile using make -j [number of cpus] (--run option in EPACTS), which runs all instructions in parallel.
+# When submitting such Makefile to SLURM queue, you need to specify the number of CPUs that will be used on a single machine (since make -j can't run parallel jobs distributed across multiple machines).
+# The script below submits EPACTS jobs into SLURM queue for each chromosome separately, and allocates 8 CPUs for each chromosome (4Gb per CPU).
+# Thus, in total there will be 176 (22 * 8) parallel jobs.
+
+
+partition=nomosix
+cpus=8
+mb=4000
+stest=q.emmax
+ped_file=
+pheno_name=
+kinship_matrix=
+
+for chr in `seq 1 22`
+do
+  sbatch -p ${partition} -J ${chr} --ntasks=1 --cpus-per-task=${cpus} --mem-per-cpu=${mb} --wrap="epacts single -vcf ${chr}.vcf.gz \
+  -ped ${ped_file} --pheno ${pheno_name} \
+  -out ${chr}.${pheno_name} \
+  -test ${stest} \
+  -kinf ${kinship_matrix} --chr ${chr} \
+  -field DS \
+  --run ${cpus}" -o ${chr}.slurm.out
+done