.gitlab-ci.yml

@@ -36,7 +36,7 @@ image:
 
 ## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST
 
-    
+
 #####################
 # Image analysis
 #####################
@@ -67,6 +67,7 @@ include:
 
 include:
   - local: "yaml-files/analysissuites/deeptools-deploy.yaml"
+  - local: "yaml-files/analysissuites/samtools-deploy.yaml"
 
 
 #####################

recipes/analysissuites/picardtools/Singularity.picardtools-2221

-BootStrap: docker
-From: ubuntu:bionic
-
-%help
-
-	This singularity installs picard tools v 2.22.1
-
-%post
-    # ~~~~~~ General setup and folder creation ~~~~~~ #
-    
-    apt-get update && apt-get install -y wget libreadline-dev
-        
-    export LC_ALL=C
-    export LC_CTYPE=C 
-    export LC_COLLATE=C 
-    export LC_TIME=C
-    export LC_MESSAGES=C
-    export LC_MONETARY=C
-    export LC_PAPER=C 
-    export LC_MEASUREMENT=C
-	
-    # ~~~~~ MINICONDA ~~~~~ #
-    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /conda && \
-    rm -f Miniconda3-latest-Linux-x86_64.sh
-    export PATH="/conda/bin:${PATH}"
-    
-    # ~~~~ R v 4.1.2 ~~~~~~ #
-    conda install -c conda-forge r-base=4.1.2
-    
-    # ~~~~~ PICARD TOOLS ~~~~~ #
-	conda install -y -c bioconda picard=2.22.1
-	
-	
-%environment
-    export PATH="${PATH}:/conda/bin"
-	export LC_ALL=C
-    export LC_CTYPE=C 
-    export LC_COLLATE=C 
-    export LC_TIME=C
-    export LC_MESSAGES=C
-    export LC_MONETARY=C
-    export LC_PAPER=C 
-    export LC_MEASUREMENT=C
-
-%labels
-	Author Nicolas Descostes
-	Version v0.0.1
-
-
-

recipes/analysissuites/picardtools/Singularity.picardtools-2271

-BootStrap: docker
-From: ubuntu:bionic
-
-%help
-
-	This singularity installs picard tools v 2.27.1
-
-%post
-    # ~~~~~~ General setup and folder creation ~~~~~~ #
-    
-    apt-get update && apt-get install -y wget libreadline-dev
-        
-    export LC_ALL=C
-    export LC_CTYPE=C 
-    export LC_COLLATE=C 
-    export LC_TIME=C
-    export LC_MESSAGES=C
-    export LC_MONETARY=C
-    export LC_PAPER=C 
-    export LC_MEASUREMENT=C
-	
-    # ~~~~~ MINICONDA ~~~~~ #
-    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /conda && \
-    rm -f Miniconda3-latest-Linux-x86_64.sh
-    export PATH="/conda/bin:${PATH}"
-    
-    # ~~~~ R v 4.1.2 ~~~~~~ #
-    conda install -c conda-forge r-base=4.1.2
-    
-    # ~~~~~ PICARD TOOLS ~~~~~ #
-	conda install -y -c bioconda picard=2.27.1
-	
-	
-%environment
-    export PATH="${PATH}:/conda/bin"
-	export LC_ALL=C
-    export LC_CTYPE=C 
-    export LC_COLLATE=C 
-    export LC_TIME=C
-    export LC_MESSAGES=C
-    export LC_MONETARY=C
-    export LC_PAPER=C 
-    export LC_MEASUREMENT=C
-
-%labels
-	Author Nicolas Descostes
-	Version v0.0.1

recipes/analysissuites/samtools/Singularity.samtools-114

+Bootstrap: docker
+From: bschiffthaler/samtools:1.14
+
+%runscript
+    echo "Running container bschiffthaler/samtools:1.14, samtools v1.14"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes

yaml-files/analysissuites/samtools-deploy.yaml

+samtools-114-builddeploy:
+  extends: .templateBuildDeploy
+  variables:
+    BASENAME: samtools
+    TAG: 114
+    RECIPE_PATH: recipes/analysissuites/samtools
+  only:
+    changes:
+      - recipes/analysissuites/samtools/Singularity.samtools-114

yaml-files/analysissuites/samtools-test.backup

+
+samtools-114-test:
+  extends: .templateTest
+  variables:
+    BASENAME: samtools
+    TAG: 114
+    RECIPE_PATH: recipes/analysissuites/samtools