diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 5dfd4fe92728c55f5d344413313c881527c8ae23..4bd03957b858f4bd84f4fb23ef7bf81d944c6b45 100644 --- a/.gitlab-ci.yml +++ b/.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 diff --git a/recipes/rpackages/bioconductor/genomeinfodb/Singularity.genomeinfodb-1323 b/recipes/rpackages/bioconductor/genomeinfodb/Singularity.genomeinfodb-1323 new file mode 100644 index 0000000000000000000000000000000000000000..61ec7c932183624b6563bba38ed99a84641d1a25 --- /dev/null +++ b/recipes/rpackages/bioconductor/genomeinfodb/Singularity.genomeinfodb-1323 @@ -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:${PATH}" + + # ~~~~~ R v 4.1.1 ~~~~~ # + conda install -c conda-forge r-base=4.1.1 + + # ~~~~~ R packages ~~~~~ # + R --slave -e 'install.packages("BiocManager", repos="https://cloud.r-project.org/")' + R --slave -e 'BiocManager::install("GenomeInfoDb")' + +%environment + export PATH="${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 diff --git a/recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480 b/recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480 new file mode 100644 index 0000000000000000000000000000000000000000..9fadc1610a0873cae57de1dab38d8154bde9a0b7 --- /dev/null +++ b/recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480 @@ -0,0 +1,49 @@ +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 + diff --git a/yaml-files/rpackages/bedtools/bedr-deploy.yaml b/yaml-files/rpackages/bedtools/bedr-deploy.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6e74b17f18e917f48e58c33b3d7e4c9ca7cf7125 --- /dev/null +++ b/yaml-files/rpackages/bedtools/bedr-deploy.yaml @@ -0,0 +1,9 @@ +bedr-107-builddeploy: + extends: .templateBuildDeploy + variables: + BASENAME: bedr + TAG: 107 + RECIPE_PATH: recipes/rpackages/bedtools + only: + changes: + - recipes/rpackages/bedtools/Singularity.bedr-107 diff --git a/yaml-files/rpackages/bedtools/bedr-test.backup b/yaml-files/rpackages/bedtools/bedr-test.backup new file mode 100644 index 0000000000000000000000000000000000000000..4fbb47041b2358f7cdcc07522006554b4815f880 --- /dev/null +++ b/yaml-files/rpackages/bedtools/bedr-test.backup @@ -0,0 +1,6 @@ +bedr-107-test: + extends: .templateTest + variables: + BASENAME: bedr + TAG: 107 + RECIPE_PATH: recipes/rpackages/bedtools diff --git a/yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-deploy.yaml b/yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-deploy.yaml new file mode 100644 index 0000000000000000000000000000000000000000..27ab2e04c0f653e9dbc3d4f1f85b385ef2ccf2fd --- /dev/null +++ b/yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-deploy.yaml @@ -0,0 +1,9 @@ +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 diff --git a/yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-test.backup b/yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-test.backup new file mode 100644 index 0000000000000000000000000000000000000000..6c3aac79cf1dc0b93f004136575a3236788b46e8 --- /dev/null +++ b/yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-test.backup @@ -0,0 +1,6 @@ +genomeinfodb-1323-test: + extends: .templateTest + variables: + BASENAME: genomeinfodb + TAG: 1323 + RECIPE_PATH: recipes/rpackages/bioconductor/genomeinfodb diff --git a/yaml-files/rpackages/bioconductor/genomicranges/genomicranges-deploy.yaml b/yaml-files/rpackages/bioconductor/genomicranges/genomicranges-deploy.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7e15aab82b9962c79d6eb241c86966177c01a12d --- /dev/null +++ b/yaml-files/rpackages/bioconductor/genomicranges/genomicranges-deploy.yaml @@ -0,0 +1,9 @@ +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 diff --git a/yaml-files/rpackages/bioconductor/genomicranges/genomicranges-test.backup b/yaml-files/rpackages/bioconductor/genomicranges/genomicranges-test.backup new file mode 100644 index 0000000000000000000000000000000000000000..4fce7ae18de0e2120eed3d5729fe27f893d7f948 --- /dev/null +++ b/yaml-files/rpackages/bioconductor/genomicranges/genomicranges-test.backup @@ -0,0 +1,6 @@ +genomicranges-1480-test: + extends: .templateTest + variables: + BASENAME: genomicranges + TAG: 1480 + RECIPE_PATH: recipes/rpackages/bioconductor/genomicranges