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Tools template #830

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Tools template #830

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fe30653
remove docker volumes, make template
mira-miracoli Jul 5, 2023
f7c0532
tools as template
mira-miracoli Jul 5, 2023
7c0011f
python2 for srma
mira-miracoli Jul 5, 2023
0d38991
Add workaround for files that are converted into templates to TPV dry…
kysrpex Jul 5, 2023
09b4d41
Update files/galaxy/tpv/tools.yml.j2
mira-miracoli Jul 5, 2023
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7 changes: 7 additions & 0 deletions .github/workflows/tpv.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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')
Expand All @@ -329,6 +330,12 @@ jobs:
subprocess.run(
["git", "checkout", "${{ steps.commits-infrastructure-playbook.outputs.before }}"]
)
# workaround for files that are converted into templates
templates = tuple(
(src, dest)
for src, dest in templates
if Path(src).exists()
)
playbook = make_playbook('sn06.yml', templates=templates)
with open(os.environ["GITHUB_OUTPUT"], "a") as file:
file.write(f"old={playbook}\n")
Expand Down
11 changes: 7 additions & 4 deletions files/galaxy/tpv/tools.yml → files/galaxy/tpv/tools.yml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -642,7 +642,6 @@ tools:
params:
submit_requirements: 'GalaxyGroup == "compute_mothur"'
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_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:
Expand All @@ -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,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_default_container_id: centos:8.3.2011
scheduling:
require:
Expand All @@ -667,7 +665,6 @@ tools:
'.*bioext_bam2msa.*':
params:
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_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:
Expand All @@ -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:
Expand Down Expand Up @@ -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"
4 changes: 2 additions & 2 deletions group_vars/sn06.yml
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Expand Up @@ -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"
Expand Down Expand Up @@ -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"