diff --git a/.github/workflows/tpv.yml b/.github/workflows/tpv.yml index bb83c2705..8529957f7 100644 --- a/.github/workflows/tpv.yml +++ b/.github/workflows/tpv.yml @@ -303,6 +303,7 @@ jobs: import os import subprocess import sys + from pathlib import Path # import make_playbook from tpv.py spec = importlib.util.spec_from_file_location('tpv_ci', '.github/workflows/tpv.py') @@ -329,6 +330,12 @@ jobs: subprocess.run( ["git", "checkout", "${{ steps.commits-infrastructure-playbook.outputs.before }}"] ) + # workaround for files that are converted into templates + templates = tuple( + (src, dest) + for src, dest in templates + if Path(src).exists() + ) playbook = make_playbook('sn06.yml', templates=templates) with open(os.environ["GITHUB_OUTPUT"], "a") as file: file.write(f"old={playbook}\n") diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml.j2 similarity index 92% rename from files/galaxy/tpv/tools.yml rename to files/galaxy/tpv/tools.yml.j2 index ae5a9af48..8db398db6 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml.j2 @@ -642,7 +642,6 @@ tools: params: submit_requirements: 'GalaxyGroup == "compute_mothur"' docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100 - docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro" docker_default_container_id: centos:8.3.2011 scheduling: require: @@ -656,7 +655,6 @@ tools: params: submit_requirements: 'GalaxyGroup == "compute_mothur"' docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100 - docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro" docker_default_container_id: centos:8.3.2011 scheduling: require: @@ -667,7 +665,6 @@ tools: '.*bioext_bam2msa.*': params: docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100 - docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro" docker_default_container_id: centos:8.3.2011 scheduling: require: @@ -677,7 +674,6 @@ tools: 'last_*': params: docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100 - docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro" docker_default_container_id: centos:8.3.2011 scheduling: require: @@ -890,3 +886,10 @@ tools: scheduling: require: - singularity + + ".*srma_wrapper.*": + scheduling: + require: + - singularity + params: + singularity_default_container_id: "{{ cvmfs.singularity.path }}/all/python:2.7.16" diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml index 1f3efb308..aa060601e 100644 --- a/group_vars/sn06.yml +++ b/group_vars/sn06.yml @@ -542,8 +542,6 @@ galaxy_config_files: dest: "{{ galaxy_config_dir }}/echo_main_env.xml" - src: "{{ galaxy_config_file_src_dir }}/tpv/tool_defaults.yml" dest: "{{ tpv_mutable_dir }}/tool_defaults.yml" - - src: "{{ galaxy_config_file_src_dir }}/tpv/tools.yml" - dest: "{{ tpv_mutable_dir }}/tools.yml" - src: "{{ galaxy_config_file_src_dir }}/tpv/roles.yml" dest: "{{ tpv_mutable_dir }}/roles.yml" - src: "{{ galaxy_config_file_src_dir }}/tpv/interactive_tools.yml" @@ -594,3 +592,5 @@ galaxy_config_templates: dest: "{{ galaxy_config['galaxy']['object_store_config_file'] }}" - src: "{{ galaxy_config_file_src_dir }}/tpv/destinations.yml.j2" dest: "{{ tpv_mutable_dir }}/destinations.yml" + - src: "{{ galaxy_config_file_src_dir }}/tpv/tools.yml.j2" + dest: "{{ tpv_mutable_dir }}/tools.yml"