replace by main

.gitlab-ci.yml

@@ -35,12 +35,7 @@ image:
 #####################
 
 ## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST
-bedr-107-test:
-  extends: .templateTest
-  variables:
-    BASENAME: bedr
-    TAG: 107
-    RECIPE_PATH: recipes/rpackages/bedtools
+
 
 #####################
 ## Include
@@ -83,6 +78,9 @@ include:
    # R packages
    #####################
   - local: "yaml-files/rpackages/snakemake-pipelines/chipseq/snakemakechipseq-deploy.yaml"
+  - local: "yaml-files/rpackages/bedtools/bedr-deploy.yaml"
+  - local: "yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-deploy.yaml"
+  - local: "yaml-files/rpackages/bioconductor/genomicranges/genomicranges-deploy.yaml"
   
    #####################
    # Single cell genomics

recipes/rpackages/bioconductor/genomeinfodb/Singularity.genomeinfodb-1323

+BootStrap: docker
+From: ubuntu:bionic
+
+%help
+
+    This singularity installs R v 4.1.1 and required packages
+
+%post
+    # ~~~~~~ General setup and folder creation ~~~~~~ #
+    
+    apt-get update && apt-get install -y wget build-essential libxml2
+    
+    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/Miniconda3-4.7.12.1-Linux-x86_64.sh && \
+    bash Miniconda3-4.7.12.1-Linux-x86_64.sh -b -p /conda && \
+    rm -f Miniconda3-4.7.12.1-Linux-x86_64.sh
+    export PATH="/conda/bin:${PATH}"
+    
+    # ~~~~~ R v 4.1.1 ~~~~~ #
+    conda install -c conda-forge r-base=4.1.1
+    
+    # ~~~~~ R packages ~~~~~ #
+    R --slave -e 'install.packages("BiocManager", repos="https://cloud.r-project.org/")'
+    R --slave -e 'BiocManager::install("GenomeInfoDb")'
+    
+%environment
+    export PATH="${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/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480

+BootStrap: docker
+From: ubuntu:bionic
+
+%help
+
+    This singularity installs R v 4.1.1 and required packages
+
+%post
+    # ~~~~~~ General setup and folder creation ~~~~~~ #
+    
+    apt-get update && apt-get install -y wget build-essential libxml2
+    
+    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/Miniconda3-4.7.12.1-Linux-x86_64.sh && \
+    bash Miniconda3-4.7.12.1-Linux-x86_64.sh -b -p /conda && \
+    rm -f Miniconda3-4.7.12.1-Linux-x86_64.sh
+    export PATH="/conda/bin:${PATH}"
+    
+    # ~~~~~ R v 4.1.1 ~~~~~ #
+    conda install -c conda-forge r-base=4.1.1
+    
+    # ~~~~~ R packages ~~~~~ #
+    R --slave -e 'install.packages("BiocManager", repos="https://cloud.r-project.org/")'
+    R --slave -e 'BiocManager::install("GenomicRanges")'
+    
+%environment
+    export PATH="${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
+

yaml-files/rpackages/bedtools/bedr-deploy.yaml

+bedr-107-builddeploy:
+  extends: .templateBuildDeploy
+  variables:
+    BASENAME: bedr
+    TAG: 107
+    RECIPE_PATH: recipes/rpackages/bedtools
+  only:
+    changes:
+      - recipes/rpackages/bedtools/Singularity.bedr-107

yaml-files/rpackages/bedtools/bedr-test.backup

+bedr-107-test:
+  extends: .templateTest
+  variables:
+    BASENAME: bedr
+    TAG: 107
+    RECIPE_PATH: recipes/rpackages/bedtools

yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-deploy.yaml

+genomeinfodb-1323-builddeploy:
+  extends: .templateBuildDeploy
+  variables:
+    BASENAME: genomeinfodb
+    TAG: 1323
+    RECIPE_PATH: recipes/rpackages/bioconductor/genomeinfodb
+  only:
+    changes:
+      - recipes/rpackages/bioconductor/genomeinfodb/Singularity.genomeinfodb-1323

yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-test.backup

+genomeinfodb-1323-test:
+  extends: .templateTest
+  variables:
+    BASENAME: genomeinfodb
+    TAG: 1323
+    RECIPE_PATH: recipes/rpackages/bioconductor/genomeinfodb

yaml-files/rpackages/bioconductor/genomicranges/genomicranges-deploy.yaml

+genomicranges-1480-builddeploy:
+  extends: .templateBuildDeploy
+  variables:
+    BASENAME: genomicranges
+    TAG: 1480
+    RECIPE_PATH: recipes/rpackages/bioconductor/genomicranges
+  only:
+    changes:
+      - recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480

yaml-files/rpackages/bioconductor/genomicranges/genomicranges-test.backup

+genomicranges-1480-test:
+  extends: .templateTest
+  variables:
+    BASENAME: genomicranges
+    TAG: 1480
+    RECIPE_PATH: recipes/rpackages/bioconductor/genomicranges