From 44a56cd4159518d84a67e52a6c17d115ebffa17b Mon Sep 17 00:00:00 2001
From: Matthys Potgieter <matthys.potgieter@gmail.com>
Date: Tue, 22 Aug 2023 13:29:35 +0000
Subject: [PATCH] fixing docker image

---
 docker/bio/Dockerfile              | 5 +++++
 docker/bio/build.sh                | 2 +-
 docker/mqproteogenomics/Dockerfile | 2 +-
 docker/mqproteogenomics/dev.sh     | 8 ++------
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/docker/bio/Dockerfile b/docker/bio/Dockerfile
index a22f7bc..370a27b 100644
--- a/docker/bio/Dockerfile
+++ b/docker/bio/Dockerfile
@@ -147,4 +147,9 @@ ENV PATH=/home/bio/miniconda3/bin:${PATH}
 ENV PYTHONPATH $PYTHONPATH::/home/bio/lib
 ENV PATH $PATH::/home/bio/bin/python:/home/bio/bin/R:/home/bio/bin/bash:/home/bio/bin/python:/home/bio/bin/perl
 
+USER root
+RUN conda init
+ENV PATH=/home/bio/miniconda3/bin:${PATH} 
+ENV PYTHONPATH $PYTHONPATH::/home/bio/lib
+ENV PATH $PATH::/home/bio/bin/python:/home/bio/bin/R:/home/bio/bin/bash:/home/bio/bin/python:/home/bio/bin/perl
 
diff --git a/docker/bio/build.sh b/docker/bio/build.sh
index 562c299..e36aafc 100755
--- a/docker/bio/build.sh
+++ b/docker/bio/build.sh
@@ -2,7 +2,7 @@
 set -e
 
 # Change build context to the root of the directory
-version=v3.0.17
+version=v3.0.19
 name=bio
 docker pull thyscbio/${name}:${version} && echo "version exists" && exit 1 || echo "Gonna build."
 cd ../..
diff --git a/docker/mqproteogenomics/Dockerfile b/docker/mqproteogenomics/Dockerfile
index 0ff4976..2c327ac 100644
--- a/docker/mqproteogenomics/Dockerfile
+++ b/docker/mqproteogenomics/Dockerfile
@@ -1,5 +1,5 @@
 #FROM thyscbio/bio:v2.10
-FROM thyscbio/bio:v3.0.9
+FROM thyscbio/bio:v3.0.17
 
 # samtools etc
 #RUN apt-get update && apt-get install -y libssl-dev openssl
diff --git a/docker/mqproteogenomics/dev.sh b/docker/mqproteogenomics/dev.sh
index 589fb9f..7ee1ca5 100755
--- a/docker/mqproteogenomics/dev.sh
+++ b/docker/mqproteogenomics/dev.sh
@@ -1,13 +1,9 @@
 #!/bin/bash
 set -a
-version=v3.0.16
+version=v3.0.19
 
 home=/home/$(who -m | awk '{print $1;}')
 config=${home}/.proteomics-pipelines_profile
 source $config
 
-DEV_PYTHONPATH=${PROTEOMICS_PIPELINES_PATH}/lib/
-
-DEV_PATH="$PATH::${PROTEOMICS_PIPELINES_PATH}/bin/python/:${PROTEOMICS_PIPELINES_PATH}/bin/R:${PROTEOMICS_PIPELINES_PATH}/bin/bash/:${PROTEOMICS_PIPELINES_PATH}/bin/perl/"
-
-docker run -it --rm -p 8181:9090 -e PYTHONPATH=${DEV_PYTHONPATH} -e PATH=${DEV_PATH} -v ${CBIO_PROTEOGENOMICS_TESTS_PATH}:${CBIO_PROTEOGENOMICS_TESTS_PATH} -v ${PROTEOMICS_PIPELINES_PATH}:${PROTEOMICS_PIPELINES_PATH} thyscbio/bio:${version}  /bin/bash 
+docker run  -it --rm -p 8181:9090 -v ${CBIO_PROTEOGENOMICS_TESTS_PATH}:${CBIO_PROTEOGENOMICS_TESTS_PATH} -v ${PROTEOMICS_PIPELINES_PATH}/bin:/home/bio/bin -v ${PROTEOMICS_PIPELINES_PATH}/lib:/home/bio/lib thyscbio/bio:${version}  /bin/bash