From 474cd3843b94c9711f506b1dc96340eabcd34510 Mon Sep 17 00:00:00 2001
From: descoste <nicolas.descostes@embl.it>
Date: Wed, 25 Jan 2023 09:35:45 +0100
Subject: [PATCH] replace by main
---
.gitlab-ci.yml | 10 ++--
.../Singularity.genomeinfodb-1323 | 48 ++++++++++++++++++
.../Singularity.genomicranges-1480 | 49 +++++++++++++++++++
.../rpackages/bedtools/bedr-deploy.yaml | 9 ++++
.../rpackages/bedtools/bedr-test.backup | 6 +++
.../genomeinfodb/genomeinfodb-deploy.yaml | 9 ++++
.../genomeinfodb/genomeinfodb-test.backup | 6 +++
.../genomicranges/genomicranges-deploy.yaml | 9 ++++
.../genomicranges/genomicranges-test.backup | 6 +++
9 files changed, 146 insertions(+), 6 deletions(-)
create mode 100644 recipes/rpackages/bioconductor/genomeinfodb/Singularity.genomeinfodb-1323
create mode 100644 recipes/rpackages/bioconductor/genomicranges/Singularity.genomicranges-1480
create mode 100644 yaml-files/rpackages/bedtools/bedr-deploy.yaml
create mode 100644 yaml-files/rpackages/bedtools/bedr-test.backup
create mode 100644 yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-deploy.yaml
create mode 100644 yaml-files/rpackages/bioconductor/genomeinfodb/genomeinfodb-test.backup
create mode 100644 yaml-files/rpackages/bioconductor/genomicranges/genomicranges-deploy.yaml
create mode 100644 yaml-files/rpackages/bioconductor/genomicranges/genomicranges-test.backup
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5dfd4fe..4bd0395 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 0000000..61ec7c9
--- /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 0000000..9fadc16
--- /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 0000000..6e74b17
--- /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 0000000..4fbb470
--- /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 0000000..27ab2e0
--- /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 0000000..6c3aac7
--- /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 0000000..7e15aab
--- /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 0000000..4fce7ae
--- /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
--
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