From 24f2ba4a7f38162aa38ea488e6a7e107f9b2bda9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 7 Sep 2020 09:48:40 +0200
Subject: [PATCH] add option in container script

---
 docker_analysis.sh      | 2 +-
 singularity_analysis.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docker_analysis.sh b/docker_analysis.sh
index d701a02..b3ffa65 100755
--- a/docker_analysis.sh
+++ b/docker_analysis.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-R_CMD="-e criblejurkat::analysis(\"/root/\")"
+R_CMD="-e criblejurkat::analysis(\"/root/${1}\")"
 docker run -it --volume $(pwd):/root/ lbmc/criblejurkat:1.0.0 R $R_CMD
 BASH_CMD="-e system(\"chown -R $(id -u ${USER}) /root/\")"
 docker run -it --volume $(pwd):/root/ lbmc/criblejurkat:1.0.0 R $BASH_CMD
diff --git a/singularity_analysis.sh b/singularity_analysis.sh
index 997b560..786b1ee 100755
--- a/singularity_analysis.sh
+++ b/singularity_analysis.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
-R_CMD="-e criblejurkat::analysis(\"$(pwd)\")"
+R_CMD="-e criblejurkat::analysis(\"${1}\")"
 singularity exec docker://lbmc/criblejurkat:1.0.0 R $R_CMD
-- 
GitLab