From e387529965480c57c1a8be2ba8e261d7d7f03956 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Sat, 25 Feb 2023 19:59:17 +0100
Subject: [PATCH] docker: Further modifications.
---
.gitlab-ci.yml | 29 ++++++++++++-----------------
DESCRIPTION | 2 +-
Dockerfile | 7 ++++---
docker/isb401/Dockerfile | 9 +++++----
docker/isb401_base/Dockerfile | 6 +++---
5 files changed, 25 insertions(+), 28 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9d3eedb..bd5c882 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,13 +42,15 @@ variables:
ISB401_RELEASE_IMAGE: $CI_REGISTRY_IMAGE:isb401_$CI_COMMIT_TAG
+
base-image:
tags:
- docker
- $RUNNER_TAG
stage: dep_images
rules:
- - changes:
+ - if: $CI_COMMIT_TAG == ""
+ changes:
- docker/base/Dockerfile
script:
- cd docker/base
@@ -64,7 +66,8 @@ ssuser-image:
- job: base-image
optional: true
rules:
- - changes:
+ - if: $CI_COMMIT_TAG == ""
+ changes:
- docker/ssuser/Dockerfile
script:
- cd docker/ssuser
@@ -80,7 +83,8 @@ isb401-base-image:
- job: ssuser-image
optional: true
rules:
- - changes:
+ - if: $CI_COMMIT_TAG == ""
+ changes:
- docker/isb401_base/Dockerfile
script:
- cd docker/isb401_base
@@ -96,9 +100,6 @@ build:
script:
- docker build --pull -t $TEST_IMAGE .
- docker push $TEST_IMAGE
- only:
- - devel
- - master
build-isb401:
tags:
@@ -109,11 +110,8 @@ build-isb401:
- job: build
script:
- cp docker/isb401/Dockerfile .
- - docker build --pull -t ISB401_TEST_IMAGE .
- - docker push ISB401_TEST_IMAGE
- only:
- - devel
- - master
+ - docker build --pull -t $ISB401_TEST_IMAGE .
+ - docker push $ISB401_TEST_IMAGE
test:
tags:
@@ -130,11 +128,8 @@ test-isb401:
- $RUNNER_TAG
stage: test
script:
- - docker pull $TEST_ISB401_IMAGE
- - docker run $TEST_ISB401_IMAGE test
- only:
- - devel
- - master
+ - docker pull $ISB401_TEST_IMAGE
+ - docker run $ISB401_TEST_IMAGE test
release-image:
tags:
@@ -143,7 +138,7 @@ release-image:
stage: release
script:
- docker pull $TEST_IMAGE
- - docker tag $TEST_IMAGE $CONTAINER_RELEASE_IMAGE
+ - docker tag $TEST_IMAGE $RELEASE_IMAGE
- docker push $RELEASE_IMAGE
rules:
- if: $CI_COMMIT_TAG =~ /^v[0-9]+.[0-9]+.[0-9]+/
diff --git a/DESCRIPTION b/DESCRIPTION
index 9f0b3a6..a039287 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: shinyscreen
Title: Pre-screening of Mass Spectrometry Data
-Version: 1.3.17
+Version: 1.3.18
Author: Todor Kondić
Maintainer: Todor Kondić <todor.kondic@uni.lu>
Authors@R:
diff --git a/Dockerfile b/Dockerfile
index d83fbf2..722fc92 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,12 +5,13 @@ ENV SS_MF_DB="PubChemLite_exposomics.csv"
ENV SS_CPU 2
ADD . shinyscreen/
RUN R CMD build shinyscreen
+USER root
RUN R CMD INSTALL shinyscreen
+USER ssuser
RUN cp shinyscreen/runme /home/ssuser/runme
-RUN cp -R shinyscreen /home/ssuser
RUN chmod u+x /home/ssuser/runme
-RUN chown ssuser /home/ssuser/runme
-RUN chown -R ssuser /home/ssuser/shinyscreen
+# RUN chown ssuser /home/ssuser/runme
+# RUN chown -R ssuser /home/ssuser/shinyscreen
RUN R -e 'library(shinyscreen);setwd("~");init(top_data_dir="~/top_data_dir",projects="~/projects",users_dir="~/users",metfrag_db_dir=Sys.getenv("SS_MF_DB_DIR"),metfrag_jar="/usr/local/bin/MetFragCommandLine.jar",no_structure_plots=T,save=T,merge=F)'
ENTRYPOINT ["/home/ssuser/runme"]
CMD ["app"]
diff --git a/docker/isb401/Dockerfile b/docker/isb401/Dockerfile
index 55fdbe1..1770df7 100644
--- a/docker/isb401/Dockerfile
+++ b/docker/isb401/Dockerfile
@@ -1,4 +1,4 @@
-FROM gitlab.lcsb.uni.lu:4567/eci/shinyscreen/deb/isb401_base:latest
+FROM gitlab.lcsb.uni.lu:4567/eci/shinyscreen/dep/isb401_base:latest
MAINTAINER todor.kondic@uni.lu
EXPOSE 5432
@@ -6,12 +6,13 @@ ENV SS_MF_DB="PubChemLite_exposomics.csv"
ENV SS_CPU 2
ADD . shinyscreen/
RUN R CMD build shinyscreen
+USER root
RUN R CMD INSTALL shinyscreen
+USER ssuser
RUN cp shinyscreen/runme /home/ssuser/runme
-RUN cp -R shinyscreen /home/ssuser
RUN chmod u+x /home/ssuser/runme
-RUN chown ssuser /home/ssuser/runme
-RUN chown -R ssuser /home/ssuser/shinyscreen
+# RUN chown ssuser /home/ssuser/runme
+# RUN chown -R ssuser /home/ssuser/shinyscreen
RUN R -e 'library(shinyscreen);setwd("~");init(top_data_dir="~/top_data_dir",projects="~/projects",users_dir="~/users",metfrag_db_dir=Sys.getenv("SS_MF_DB_DIR"),metfrag_jar="/usr/local/bin/MetFragCommandLine.jar",no_structure_plots=T,save=T,merge=F)'
ENTRYPOINT ["/home/ssuser/runme"]
CMD ["app"]
\ No newline at end of file
diff --git a/docker/isb401_base/Dockerfile b/docker/isb401_base/Dockerfile
index c699e35..ffbdbef 100644
--- a/docker/isb401_base/Dockerfile
+++ b/docker/isb401_base/Dockerfile
@@ -1,12 +1,12 @@
FROM gitlab.lcsb.uni.lu:4567/eci/shinyscreen/dep/ssuser:latest
MAINTAINER todor.kondic@uni.lu
-WORKDIR isb401/top_data_dir/isb401
+RUN mkdir top_data_dir/isb401
+RUN mkdir projects/isb401
+WORKDIR top_data_dir/isb401
RUN curl -LJO https://zenodo.org/record/3666069/files/ISB401_AA_Std_pos.mzML
RUN curl -LJO https://zenodo.org/record/3666069/files/ISB401_KO_pos.mzML
RUN curl -LJO https://zenodo.org/record/3666069/files/ISB401_WT_pos.mzML
WORKDIR /home/ssuser/
RUN curl -LJO https://gitlab.lcsb.uni.lu/eci/isb401/-/archive/master/isb401-master.tar.gz
RUN tar -xf isb401-master.tar.gz
-RUN mkdir top_data_dir/isb401
-RUN mkdir projects/isb401
RUN cp isb401-master/shinyscreen_files/*.csv /home/ssuser/projects/isb401
\ No newline at end of file
--
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