From 9e3b0b5d5bb17a5de61f85a3fff1f9e82578803f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 16 Mar 2023 16:10:49 +0100
Subject: [PATCH] add mbelari_count_small.slurm

---
 src/mbelari_count_small.slurm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 src/mbelari_count_small.slurm

diff --git a/src/mbelari_count_small.slurm b/src/mbelari_count_small.slurm
new file mode 100644
index 0000000..0252a47
--- /dev/null
+++ b/src/mbelari_count_small.slurm
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=mbelari_count    # Nom du jobe
+#SBATCH --output=%j.log   # Standard output et error log
+#SBATCH --time=2-00:00:00             # Délai max = 7 jours
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=10
+#SBATCH --mem=200G
+#SBATCH --partition=Lake
+
+
+cd /scratch/Bio/lmodolo/kmer_diff/
+
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+WORK=$(pwd)
+
+# kmdiff count
+${KMDIFF} count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 10
+
-- 
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