Merge pull request #252 from ewels/master

NGI-MethylSeq - use singularity image.
NationalGenomicsInfrastructure · Sep 19, 2017 · f5db90a · f5db90a
2 parents 56ba684 + dcf0fd4
commit f5db90a
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Showing 3 changed files with 14 additions and 2 deletions.
diff --git a/roles/ngi-methylseq/defaults/main.yml b/roles/ngi-methylseq/defaults/main.yml
@@ -1,3 +1,4 @@
 ngi_methylseq_dest: "{{ sw_path }}/ngi-methylseq"
 ngi_methylseq_repo: "https://github.com/SciLifeLab/NGI-MethylSeq.git"
-ngi_methylseq_version: "0.3"
+ngi_methylseq_docker: "docker://scilifelab/ngi-methylseq"
+ngi_methylseq_version: "0.3.1"
diff --git a/roles/ngi-methylseq/tasks/main.yml b/roles/ngi-methylseq/tasks/main.yml
@@ -1,11 +1,21 @@
 ---
 
-- name: Fetch NGI-MethySeq from GitHub
+- name: Fetch NGI-MethylSeq from GitHub
   git: repo="{{ ngi_methylseq_repo }}"
        dest="{{ ngi_methylseq_dest }}"
        version="{{ ngi_methylseq_version }}"
        force=yes
 
+- name: Create NGI-MethylSeq Singularity folder
+  file: name="{{ ngi_resources }}/singularity/ngi-methylseq" state=directory mode=g+s
+
+- name: Pull NGI-MethylSeq Singularity image
+  command: "singularity pull {{ ngi_methylseq_docker }}:{{ ngi_methylseq_version }} --name ngi-methylseq-{{ ngi_methylseq_version }}.img"
+  environment:
+    SINGULARITY_CACHEDIR: "/scratch"
+  args:
+    chdir: "{{ ngi_resources }}/singularity/ngi-methylseq/"
+
 - name: Create NGI-RNAseq config
   template:
     src: "ngi-methylseq_site.config"

diff --git a/roles/ngi-methylseq/templates/ngi-methylseq_site.config b/roles/ngi-methylseq/templates/ngi-methylseq_site.config
@@ -1 +1,2 @@
 params.project = '{{ item.project_id }}'
+process.container = '{{ ngi_resources }}/singularity/ngi-methylseq/ngi-methylseq-{{ ngi_methylseq_version }}.img'
Original file line number	Diff line number	Diff line change
		@@ -1 +1,2 @@
		params.project = '{{ item.project_id }}'
		process.container = '{{ ngi_resources }}/singularity/ngi-methylseq/ngi-methylseq-{{ ngi_methylseq_version }}.img'