docker: Further modifications.

.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]+/

DESCRIPTION

 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: 

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"]

docker/isb401/Dockerfile

-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"]
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docker/isb401_base/Dockerfile

 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