diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index da7365817bd39effb980251a86d970f05d8422b9..ba6577b95298a3da8e89916793953f6bb829634a 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -36,6 +36,12 @@ image: ## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST +genomicranges-1480-test: + extends: .templateTest + variables: + BASENAME: genomicranges + TAG: 1480 + RECIPE_PATH: recipes/rpackages/bioconductor/genomicranges ##################### ## Include diff --git a/recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480 b/recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480 new file mode 100644 index 0000000000000000000000000000000000000000..22967b96ba20cadb9b3953cca170f8ceaf430464 --- /dev/null +++ b/recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480 @@ -0,0 +1,48 @@ +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