Commit 7327b8a9 authored by hjulienne's avatar hjulienne

corrected SLURM section

parent eab6512c
Pipeline #7869 passed with stages
in 1 minute and 22 seconds
......@@ -69,7 +69,7 @@ all in the same folder with the following columns with the same header:
| rs6548219| 30762 | A | G | -1.133 |
+----------+-------+------+-----+--------+
This format can be obtained with the `JASS PreProcessing package <https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing>`.
This format can be obtained with the `JASS PreProcessing package <https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing>`_.
Launching imputation on one chromosome
......@@ -79,9 +79,8 @@ RAISS has an interface with the command line (see Command Line Usage bellow).
If you have access to a cluster, an efficient way to use RAISS is to launch
the imputation of each chromosome on a separate cluster node. The script
launch_imputation_all_gwas.sh contain an example for SLURM scheduler.
#TODO check command line interface
`launch_imputation_all_gwas.sh <https://gitlab.pasteur.fr/statistical-genetics/raiss/blob/master/launch_imputation_all_gwas.sh>`_
contain an example of raiss usage with a SLURM scheduler.
Output
======
......
#!/bin/bash
#SBATCH --mem=32000
#SBATCH -o /pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/genome_imputation_script/imputation_log/IMPFJ_%a.log
#SBATCH -e /pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/genome_imputation_script/error_log/error_%a.log
#define data location
module load Python/3.6.0
output_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImFJ_imputed_zfiles"
ref_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel"
zscore_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImpG_zfiles"
ld_folder="/pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/berisa_ld_block"
args=$(head -n ${SLURM_ARRAY_TASK_ID} $1 | tail -n 1)
study=$(echo $args | cut -d' ' -f1)
chrom=$(echo $args | cut -d' ' -f2)
#quick fix to access entry point on tars
alias impute_jass="python3 /pasteur/homes/hjulienn/.local/lib/python3.6/site-packages/impute_jass/__main__.py"
#study="GIANT_HEIGHT"
#chrom="chr22"
echo "Study: ${study}; Chrom: ${chrom}"
#time impute_jass --chrom ${chrom} --gwas ${study} --ref-folder ${ref_folder} --ld-folder ${ld_folder} --zscore-folder ${zscore_folder} --output-folder ${output_folder}
time python3 /pasteur/homes/hjulienn/.local/lib/python3.6/site-packages/impute_jass/__main__.py --chrom ${chrom} --gwas ${study} --ref-folder ${ref_folder} --ld-folder ${ld_folder} --zscore-folder ${zscore_folder} --output-folder ${output_folder}
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