From 012fa5528a117ecf1856b044058e89a9c0835452 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 6 Mar 2023 10:12:18 +0100
Subject: [PATCH] add slurm script for kmdiff diff

---
 src/mbelari_diff.slurm         | 17 +++++++++++++++++
 src/mlongespiculosa_diff.slurm | 17 +++++++++++++++++
 src/mspiculigera_diff.slurm    | 18 ++++++++++++++++++
 3 files changed, 52 insertions(+)
 create mode 100644 src/mbelari_diff.slurm
 create mode 100644 src/mlongespiculosa_diff.slurm
 create mode 100644 src/mspiculigera_diff.slurm

diff --git a/src/mbelari_diff.slurm b/src/mbelari_diff.slurm
new file mode 100644
index 0000000..31c5ffc
--- /dev/null
+++ b/src/mbelari_diff.slurm
@@ -0,0 +1,17 @@
+#!/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=32
+#SBATCH --mem=128G
+#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} diff -d ${WORK}/results/mbelari_counts/ -1 1 -2 1 -t 32
diff --git a/src/mlongespiculosa_diff.slurm b/src/mlongespiculosa_diff.slurm
new file mode 100644
index 0000000..7c2eb9c
--- /dev/null
+++ b/src/mlongespiculosa_diff.slurm
@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH --job-name=mlongespiculosa_count    # Nom du jobe
+#SBATCH --output=%j.log   # Standard output et error log
+#SBATCH --time=2-00:00:00             # Délai max = 7 jours
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=32
+#SBATCH --mem=128G
+#SBATCH --partition=Lake
+
+
+cd /scratch/Bio/lmodolo/kmer_diff/
+
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+WORK=$(pwd)
+
+# kmdiff count
+${KMDIFF} diff -d ${WORK}/results/mlongespiculosa_counts/ -1 7 -2 2 -t 32
diff --git a/src/mspiculigera_diff.slurm b/src/mspiculigera_diff.slurm
new file mode 100644
index 0000000..5b561ac
--- /dev/null
+++ b/src/mspiculigera_diff.slurm
@@ -0,0 +1,18 @@
+#!/bin/bash
+#
+#SBATCH --job-name=mspiculigera_count    # Nom du jobe
+#SBATCH --output=%j.log   # Standard output et error log
+#SBATCH --time=2-00:00:00             # Délai max = 7 jours
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=32
+#SBATCH --mem=128G
+#SBATCH --partition=Lake
+
+
+cd /scratch/Bio/lmodolo/kmer_diff/
+
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+WORK=$(pwd)
+
+# kmdiff count
+${KMDIFF} diff -d ${WORK}/results/mspiculigera_counts/ -1 1 -2 1 -t 32
-- 
GitLab