From 7ec4f2009743127a4db7aae2ee460410afb45240 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Mar 2023 15:03:31 +0100
Subject: [PATCH] slurm: add abs path to ch-run
---
src/mbelari_count.slurm | 4 ++--
src/mlongespiculosa_count.slurm | 4 ++--
src/mspiculigera_count.slurm | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/src/mbelari_count.slurm b/src/mbelari_count.slurm
index 0ff6752..13ecc87 100644
--- a/src/mbelari_count.slurm
+++ b/src/mbelari_count.slurm
@@ -10,9 +10,9 @@
cd /scratch/Bio/lmodolo/kmer_diff/
-alias kmdiff="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+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 ${WORK}/results/mbelari_counts/ -t 32
+${KMDIFF} count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 32
diff --git a/src/mlongespiculosa_count.slurm b/src/mlongespiculosa_count.slurm
index bb33009..36b8853 100644
--- a/src/mlongespiculosa_count.slurm
+++ b/src/mlongespiculosa_count.slurm
@@ -10,8 +10,8 @@
cd /scratch/Bio/lmodolo/kmer_diff/
-alias kmdiff="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
WORK=$(pwd)
# kmdiff count
-kmdiff count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32
+${KMDIFF} count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32
diff --git a/src/mspiculigera_count.slurm b/src/mspiculigera_count.slurm
index be4db3a..7716bd6 100644
--- a/src/mspiculigera_count.slurm
+++ b/src/mspiculigera_count.slurm
@@ -11,8 +11,8 @@
cd /scratch/Bio/lmodolo/kmer_diff/
-alias kmdiff="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
WORK=$(pwd)
# kmdiff count
-kmdiff count -f ${WORK}/data/sample_mspiculigera.csv -d ${WORK}/results/mspiculigera_counts/ -t 32
+${KMDIFF} count -f ${WORK}/data/sample_mspiculigera.csv -d ${WORK}/results/mspiculigera_counts/ -t 32
--
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