From fe8a873aac0ba9a7a81059168a760fc349c928b6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Mar 2023 14:31:52 +0100
Subject: [PATCH] add slurm script for kmdiff count

---
 src/kmdiff.sh                   | 14 +++++++++++---
 src/mbelari_count.slurm         | 18 ++++++++++++++++++
 src/mlongespiculosa_count.slurm | 17 +++++++++++++++++
 src/mspiculigera_count.slurm    | 17 +++++++++++++++++
 4 files changed, 63 insertions(+), 3 deletions(-)
 create mode 100644 src/mbelari_count.slurm
 create mode 100644 src/mlongespiculosa_count.slurm
 create mode 100644 src/mspiculigera_count.slurm

diff --git a/src/kmdiff.sh b/src/kmdiff.sh
index 6062110..303773f 100644
--- a/src/kmdiff.sh
+++ b/src/kmdiff.sh
@@ -8,8 +8,16 @@ update_ch_image.sh
 
 alias kmdiff="ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
 
+WORK=$(pwd)
+mkdir results/
+
 # kmdiff count
+kmdiff count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 32
+kmdiff count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32
+kmdiff count -f ${WORK}/data/sample_mspiculigera.csv -d ${WORK}/results/mspiculigera_counts/ -t 32
+
+# kmdiff diff
 
-kmdiff count -f data/sample_mbelari.csv -d results/mbelari_counts/ -t 32
-kmdiff count -f data/sample_mlongespiculosa.csv -d results/mlongespiculosa_counts/ -t 32
-kmdiff count -f data/sample_mspiculigera.csv -d results/mspiculigera_counts/ -t 32
+kmdiff diff -d ${WORK}/results/mbelari_counts/ -1 7 -2 2 -t 32
+kmdiff diff -d ${WORK}/results/mlongespiculosa_counts/ -1 1 -2 1 -t 32
+kmdiff diff -d ${WORK}/results/mspiculigera_counts/ -1 1 -2 1 -t 32
diff --git a/src/mbelari_count.slurm b/src/mbelari_count.slurm
new file mode 100644
index 0000000..cdb7d65
--- /dev/null
+++ b/src/mbelari_count.slurm
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=mbelari_count    # Nom du jobe
+#SBATCH --output=%j.log   # Standard output et error log
+#SBATCH --time=2-00:00:00             # Délai max = 7 jours
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=32
+#SBATCH --mem-per-cpu=128G
+#SBATCH --partition=Lake
+
+
+cd /scratch/Bio/lmodolo/kmer_diff/
+
+alias kmdiff="ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+WORK=$(pwd)
+
+# kmdiff count
+kmdiff count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 32
+
diff --git a/src/mlongespiculosa_count.slurm b/src/mlongespiculosa_count.slurm
new file mode 100644
index 0000000..89c64d7
--- /dev/null
+++ b/src/mlongespiculosa_count.slurm
@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH --job-name=mlongespiculosa_count    # Nom du jobe
+#SBATCH --output=%j.log   # Standard output et error log
+#SBATCH --time=2-00:00:00             # Délai max = 7 jours
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=32
+#SBATCH --mem-per-cpu=128G
+#SBATCH --partition=Lake
+
+
+cd /scratch/Bio/lmodolo/kmer_diff/
+
+alias kmdiff="ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+WORK=$(pwd)
+
+# kmdiff count
+kmdiff count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32
diff --git a/src/mspiculigera_count.slurm b/src/mspiculigera_count.slurm
new file mode 100644
index 0000000..0ef0633
--- /dev/null
+++ b/src/mspiculigera_count.slurm
@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH --job-name=mspiculigera_count    # Nom du jobe
+#SBATCH --output=%j.log   # Standard output et error log
+#SBATCH --time=2-00:00:00             # Délai max = 7 jours
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=32
+#SBATCH --mem-per-cpu=128G
+#SBATCH --partition=Lake
+
+
+cd /scratch/Bio/lmodolo/kmer_diff/
+
+alias kmdiff="ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+WORK=$(pwd)
+
+# kmdiff count
+kmdiff count -f ${WORK}/data/sample_mspiculigera.csv -d ${WORK}/results/mspiculigera_counts/ -t 32
-- 
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