add slurm script for kmdiff count

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

src/mbelari_count.slurm

+#!/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
+

src/mlongespiculosa_count.slurm

+#!/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

src/mspiculigera_count.slurm

+#!/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