From 57e4cf9f32192b3ad9b8e2218c2549578b985d3e Mon Sep 17 00:00:00 2001
From: mmassaviol <mathieu.massaviol@hotmail.fr>
Date: Wed, 18 Dec 2019 11:03:30 +0100
Subject: [PATCH] Update deploys
---
Dockerfile | 5 +++--
deploy.sh => deployIFB.sh | 0
files/singularity.def | 6 +++---
waw_workflow.qsub | 3 +--
4 files changed, 7 insertions(+), 7 deletions(-)
rename deploy.sh => deployIFB.sh (100%)
diff --git a/Dockerfile b/Dockerfile
index 6b31fce..ab8b212 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -47,7 +47,8 @@ ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8
#This part is necessary to run on ISEM cluster
-RUN mkdir -p /share/apps/lib \
+RUN mkdir -p /share/apps/bin \
+ && mkdir -p /share/apps/lib \
&& mkdir -p /share/apps/gridengine \
&& mkdir -p /share/bio \
&& mkdir -p /opt/gridengine \
@@ -57,6 +58,6 @@ RUN mkdir -p /share/apps/lib \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
-
+
EXPOSE 3838
CMD ["Rscript", "-e", "setwd('/sagApp/'); shiny::runApp('/sagApp/app.R',port=3838 , host='0.0.0.0')"]
diff --git a/deploy.sh b/deployIFB.sh
similarity index 100%
rename from deploy.sh
rename to deployIFB.sh
diff --git a/files/singularity.def b/files/singularity.def
index 6ab135b..34e4f81 100644
--- a/files/singularity.def
+++ b/files/singularity.def
@@ -122,9 +122,9 @@ singularity run --app appName this_container.sif
Rscript -e 'BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE)'
mkdir -p /share/apps/bin
-mkdir /share/apps/lib
-mkdir /share/apps/gridengine
-mkdir /share/bio
+mkdir -p /share/apps/lib
+mkdir -p /share/apps/gridengine
+mkdir -p /share/bio
mkdir -p /opt/gridengine
mkdir -p /export/scrach
mkdir -p /usr/lib64
diff --git a/waw_workflow.qsub b/waw_workflow.qsub
index 50bc865..13b679e 100644
--- a/waw_workflow.qsub
+++ b/waw_workflow.qsub
@@ -19,10 +19,9 @@ resultsDir=$2
#configfile must be set to /Data/config.yaml
configFile=$3
cores=$4
-
#if we must build the image from docker image
singularity build rnaseqde.simg docker://mbbteam/rnaseqde:latest
#Run the workflow in cmd line
-singularity exec -B $dataDir:/Data -B $resultsDir:/Results rnaseqde.simg snakemake -s /workflow/Snakefile --configfile $configFile --cores $cores
\ No newline at end of file
+singularity exec -B $dataDir:/Data -B $resultsDir:/Results rnaseqde.simg snakemake -s /workflow/Snakefile --configfile $configFile --cores $cores
--
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