/
tools.yml
1371 lines (1263 loc) · 59.9 KB
/
tools.yml
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---
# ALL tags must be with dashes (-) instead of underscores (_)
tools:
basic_gpu_resource_param_tool:
# Type of compute resource (CPU or GPU) for the tool depends on user's input from its wrapper.
# Default resource is CPU.
rules:
- id: resource_params_gpu
if: |
param_dict = job.get_param_values(app)
param_dict.get('__job_resource', {}).get('__job_resource__select') == 'yes'
gpus: int(job.get_param_values(app)['__job_resource']['gpu'])
__DATA_FETCH__:
cores: 1
mem: 3
gpus: 0
scheduling:
require:
- upload
rules:
- id: no-pulsar
if: user is not None
execute: |
from tpv.core.entities import Tag, TagSetManager, TagType
user_preferences = user.extra_preferences
pulsar_tag = user_preferences.get("distributed_compute|remote_resources", "None")
pulsar_tag = Tag("scheduling", pulsar_tag, TagType.REQUIRE) if pulsar_tag != "None" else None
entity.tpv_tags.tags = [
tag
for tag in entity.tpv_tags.tags
if tag != pulsar_tag
]
env:
TEMP: /data/1/galaxy_db/tmp
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/.*:
inherits: basic_gpu_resource_param_tool
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_.*/deeptools_.*/.*:
rules:
- id: deeptools_singularity
if: |
# versions without singularity container available
no_container = {
'2.0.1.0',
'2.1.0.0',
'2.2.2.0', # a container is available but it is broken
'2.2.3.0',
'2.5.0.0',
'3.0.1.0',
'3.0.2.0',
}
all(not helpers.tool_version_eq(tool, version) for version in no_container)
scheduling:
require:
- singularity
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/.*:
rules:
- id: deeptools_singularity_bam_compare
if: |
# versions working in conda but not in singularity
conda_only_versions = {
'2.4.1.0',
}
any(helpers.tool_version_eq(tool, version) for version in conda_only_versions)
# remove singularity tag
execute: |
from tpv.core.entities import TagSetManager, TagType
entity.tpv_tags = TagSetManager([
tag for tag in entity.tpv_tags.tags
if not (tag.value == 'singularity' and tag.tag_type == TagType.REQUIRE)
])
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*:
rules:
- id: deeptools_singularity_bam_coverage
if: |
# versions working in conda but not in singularity
conda_only_versions = {
'2.4.1.0',
}
any(helpers.tool_version_eq(tool, version) for version in conda_only_versions)
# remove singularity tag
execute: |
from tpv.core.entities import TagSetManager, TagType
entity.tpv_tags = TagSetManager([
tag for tag in entity.tpv_tags.tags
if not (tag.value == 'singularity' and tag.tag_type == TagType.REQUIRE)
])
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/.*:
rules:
- id: deeptools_singularity_plot_coverage
if: |
# versions working in conda but not in singularity
conda_only_versions = {
'2.4.1.0',
}
any(helpers.tool_version_eq(tool, version) for version in conda_only_versions)
# remove singularity tag
execute: |
from tpv.core.entities import TagSetManager, TagType
entity.tpv_tags = TagSetManager([
tag for tag in entity.tpv_tags.tags
if not (tag.value == 'singularity' and tag.tag_type == TagType.REQUIRE)
])
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/.*:
rules:
- id: deeptools_singularity_plot_profile
if: |
# versions working in conda but not in singularity
conda_only_versions = {
'3.1.2.0.0',
}
any(helpers.tool_version_eq(tool, version) for version in conda_only_versions)
# remove singularity tag
execute: |
from tpv.core.entities import TagSetManager, TagType
entity.tpv_tags = TagSetManager([
tag for tag in entity.tpv_tags.tags
if not (tag.value == 'singularity' and tag.tag_type == TagType.REQUIRE)
])
toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/.*:
cores: 10
rules:
- id: hifiasm_memory
# The memory requirement of Hifiasm depends on a wrapper's input
if: |
parameters = {p.name: p.value for p in job.parameters}
parameters = tool.params_from_strings(parameters, app)
advanced_options = parameters.get("advanced_options", dict())
hg_size = advanced_options.get("hg_size", "")
bool(hg_size)
mem: |
from math import ceil
parameters = {p.name: p.value for p in job.parameters}
parameters = tool.params_from_strings(parameters, app)
advanced_options = parameters.get("advanced_options", dict())
kcov_default = 36
kcov = advanced_options.get("kcov", kcov_default)
hg_size = advanced_options.get("hg_size", "")
value = 0
if hg_size:
conversion_factors = {
"k": 1000000,
"M": 1000,
"G": 1,
}
conversion_factors = {
key.lower(): value for key, value in conversion_factors.items()
}
suffix = hg_size[-1:].lower()
value = hg_size[:len(hg_size) - 1]
value = value.replace(",", ".")
value = float(value)
# compute hg size in Gb
value = value / conversion_factors[suffix.lower()]
value = ceil(value * (kcov * 2) * 1.75)
# return the amount of memory needed
value
toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/.*:
inherits: basic_gpu_resource_param_tool
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/.*:
cores: 2
scheduling:
require:
- condor-tpv
rules:
- if: input_size >= 0.015
cores: 14
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/.*:
scheduling:
require:
- conda
- singularity
toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/.*:
cores: 8
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/rnateam/dewseq/dewseq/.*:
cores: 2
mem: 40
scheduling:
prefer:
- condor-tpv
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*:
rules:
- if: input_size >= 0.01
cores: 3
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/sirius_csifingerid/sirius_csifingerid/.*:
cores: 8
mem: 8
toolshed.g2.bx.psu.edu/repos/rnateam/htseq-clip/htseq-clip/.*:
cores: 4
mem: 16
scheduling:
prefer:
- condor-tpv
toolshed.g2.bx.psu.edu/repos/iuc/sleuth/sleuth/.*:
cores: 4
mem: 16
scheduling:
require:
- conda
- singularity
toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/.*:
cores: 12
mem: 40
scheduling:
require:
- conda
- singularity
toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/.*:
cores: 8
mem: 32
scheduling:
require:
- conda
- singularity
toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*:
cores: 10
mem: 32
rules:
- if: helpers.tool_version_eq(tool, '2.0.0+galaxy1')
# The version number of alphafold may not match the version number of the the tool in this case. The alphafold
# version number should in fact be newer than 2.1.0 and older than 2.1.1. Check the links below to verify this
# claim:
# - https://github.com/usegalaxy-au/tools-au/blob/fae57866fda74c85d405a2db03a82ebfdaed6070/tools/alphafold/docker/Dockerfile#L7
# - https://github.com/usegalaxy-au/tools-au/tree/fae57866fda74c85d405a2db03a82ebfdaed6070/tools/alphafold/docker
# - https://github.com/usegalaxy-au/tools-au/commit/aa7c146a02df64fcaa8ef03a89a76012227f35d6
# - https://github.com/deepmind/alphafold/blob/be37a41d6f83e4145bd4912cbe8bf6a24af80c29/setup.py#L21
# However neither, 2.1.0 nor 2.1.1 are still supposed to be able to use the GPU during the relaxation step, yet
# there are CUDA errors in the tool tests when no GPU is available. Verify the GPU use claim below:
# - https://github.com/deepmind/alphafold/blob/be37a41d6f83e4145bd4912cbe8bf6a24af80c29/alphafold/relax/amber_minimize.py#L93
# There seems indeed to have been a mishap when packaging this version of the tool. See the link below.
# - https://github.com/usegalaxy-au/tools-au/commit/06dd35df4064c0c3c1272957e46c0df59d24c7fe
# Regardless of how things came to be this way, this version of the tool needs a GPU, and the
# requirement cannot be disabled) because `ALPHAFOLD_USE_GPU` is not declared in alphafold.xml. Thus we set
# gpus to one.
gpus: 1
- if: helpers.tool_version_eq(tool, '2.0.0+galaxy2')
# The same story as above applies to this tool version.
# - https://github.com/usegalaxy-au/tools-au/blob/78302ce1d79058f37b24c7b395de450f42631260/tools/alphafold/alphafold.xml#L52
gpus: 1
- if: helpers.tool_version_eq(tool, '2.1.2+galaxy0')
# This version of alphafold already allows to control whether the GPU should be used during the relaxation
# step, but the tool developers added `ALPHAFOLD_USE_GPU` in the next tool revision (2.1.2+galaxy1). GPU use
# is still mandatory.
# - https://github.com/usegalaxy-au/tools-au/commit/6352c107873cf824d83bfe06b368523624746de7
gpus: 1
- if: helpers.tool_version_lt(tool, '2.3')
params:
singularity_run_extra_arguments: "--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases/2.2/,ALPHAFOLD_USE_GPU=False"
- if: helpers.tool_version_gte(tool, '2.3') and helpers.tool_version_lt(tool, '2.3.1+galaxy2')
params:
singularity_run_extra_arguments: "--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases/2.3/,ALPHAFOLD_USE_GPU=False"
- if: helpers.tool_version_gte(tool, '2.3.1+galaxy2')
execute: |
from random import SystemRandom
if SystemRandom().random() < 0.10 and not job.get_param_values(app).get("model_preset") == "multimer": # Multimer needs more memory than we can currently provide on GPU nodes
entity.gpus = 1
entity.cores = 8
# We are currently utilizing a whole GPU VM (cores 8 mem 40 gpus 1)
entity.mem = 32
entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=True'
else:
entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=False'
# tweak amount of requested memory depending on the AlphaFold model to be run
- id: model_preset_multimer
if: job.get_param_values(app).get("model_preset") == "multimer"
mem: 69
- id: cz-pulsar_alphafold
if: |
"cz-pulsar" in {tag.value for tag in entity.tpv_tags.tags}
gpus: 1
scheduling:
require:
- singularity
basic_docker_tool:
params:
submit_requirements: "GalaxyDockerHack == True"
scheduling:
require:
- docker
toolshed.g2.bx.psu.edu/repos/bgruening/cellpose/cellpose/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/.*:
# any container should work
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/iuc/chewbbaca.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/recetox/recetox_msfinder/recetox_msfinder/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/imgteam/bioformats2raw/bf2raw/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/bgruening/biomodels_biomd0000001066/biomodels_biomd0000001066/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/bgruening/biomodels_biomd0000001076/biomodels_biomd0000001076/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/imgteam/rfove/rfove/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/iuc/homer_findmotifs/homer_findMotifs/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/gga/repeatexplorer_clustering/repeatexplorer_clustering/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/galaxyp/diann/diann/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/bgruening/instagraal/instagraal/.*:
inherits: basic_docker_tool
gpus: 1
cores: 1
mem: 30
params:
docker_run_extra_arguments: ' --gpus all '
env:
GPU_AVAILABLE: 1
toolshed.g2.bx.psu.edu/repos/bgruening/whisper/whisper/.*:
inherits: basic_docker_tool
cores: 1
mem: 5
env:
OPENAI_WHISPER_MODEL_DIR: "/data/db/models/openai_whisper/"
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*:
# 8 (from the shared TPV) seems to high for me
cores: 3
toolshed.g2.bx.psu.edu/repos/ecology/cb_ivr/cb_ivr/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/ecology/taxo_cov_template/taxo_cov_template/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/ecology/makeeml/makeeml/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/ecology/entities_template/entities_template/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/ecology/eal_templates/eal_templates/.*:
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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__quality_control__evaluate_seqs/qiime2__quality_control__evaluate_seqs/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__quality_control__evaluate_taxonomy/qiime2__quality_control__evaluate_taxonomy/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__quality_control__exclude_seqs/qiime2__quality_control__exclude_seqs/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__quality_control__filter_reads/qiime2__quality_control__filter_reads/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__quality_filter__q_score/qiime2__quality_filter__q_score/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__classify_samples/qiime2__sample_classifier__classify_samples/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__classify_samples_from_dist/qiime2__sample_classifier__classify_samples_from_dist/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__classify_samples_ncv/qiime2__sample_classifier__classify_samples_ncv/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__confusion_matrix/qiime2__sample_classifier__confusion_matrix/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__fit_classifier/qiime2__sample_classifier__fit_classifier/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__fit_regressor/qiime2__sample_classifier__fit_regressor/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__heatmap/qiime2__sample_classifier__heatmap/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__metatable/qiime2__sample_classifier__metatable/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__predict_classification/qiime2__sample_classifier__predict_classification/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__predict_regression/qiime2__sample_classifier__predict_regression/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__regress_samples/qiime2__sample_classifier__regress_samples/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__regress_samples_ncv/qiime2__sample_classifier__regress_samples_ncv/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__scatterplot/qiime2__sample_classifier__scatterplot/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__split_table/qiime2__sample_classifier__split_table/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__sample_classifier__summarize/qiime2__sample_classifier__summarize/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__collapse/qiime2__taxa__collapse/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__filter_seqs/qiime2__taxa__filter_seqs/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__filter_table/qiime2__taxa__filter_table/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_closed_reference/qiime2__vsearch__cluster_features_closed_reference/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_open_reference/qiime2__vsearch__cluster_features_open_reference/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__dereplicate_sequences/qiime2__vsearch__dereplicate_sequences/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__fastq_stats/qiime2__vsearch__fastq_stats/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__merge_pairs/qiime2__vsearch__merge_pairs/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_denovo/qiime2__vsearch__uchime_denovo/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__export/qiime2_core__tools__export/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/.*:
inherits: basic_docker_tool
toolshed.g2.bx.psu.edu/repos/iuc/cherri_train/cherri_train/.*:
inherits: basic_docker_tool
cores: 10
mem: 90
toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/.*:
cores: 4
mem: 30
gpus: 1
params:
singularity_run_extra_arguments: ' --nv '
scheduling:
require:
- singularity
toolshed.g2.bx.psu.edu/repos/iuc/cherri_eval/cherri_eval/.*:
inherits: basic_docker_tool
cores: 1
mem: 20
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/.*:
cores: 2
scheduling:
accept:
- pulsar
- condor-tpv
rules:
- if: 0.05 <= input_size < 1
cores: 8
mem: 100
- if: 1 <= input_size < 60
cores: 16
mem: 350
- if: input_size >= 60
fail: Too much data, please don't use Spades for this
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*:
cores: 2
rules:
- if: 0.005 <= input_size < 1
cores: 8
mem: 100
- if: 1 <= input_size < 2
cores: 12
mem: 200
- if: 2 <= input_size < 20
cores: 20
mem: 350
scheduling:
prefer:
- condor-tpv
- if: input_size >= 20
fail: Too much data, please don't use this tool for this.
toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/.*:
cores: 8
rules:
- if: input_size < 1
mem: 15
- if: 1 <= input_size < 5
mem: 75
- if: 5 <= input_size < 10
cores: 12
mem: 150
- if: 10 <= input_size < 15
cores: 12
mem: 225
- if: 15 <= input_size < 20
cores: 12
mem: 300
- if: 20 <= input_size < 25
mem: 375
cores: 16
- if: input_size >= 25
fail: Too much data, please check if the input is correct.
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*:
# see https://github.com/usegalaxy-eu/infrastructure-playbook/pull/881 for some numbers
cores: 10
mem: 9 + input_size * 1
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
toolshed.g2.bx.psu.edu/repos/iuc/spades_rnaviralspades/spades_rnaviralspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
toolshed.g2.bx.psu.edu/repos/iuc/spades_metaplasmidspades/spades_metaplasmidspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
toolshed.g2.bx.psu.edu/repos/iuc/spades_coronaspades/spades_coronaspades/.*:
cores: 10
mem: 8
toolshed.g2.bx.psu.edu/repos/iuc/spades_biosyntheticspades/spades_biosyntheticspades/.*:
inherits: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*
# cactus suite
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_cactus/cactus_cactus/.*:
context:
test_cores: 4
cores: 20
mem: 256
scheduling:
prefer:
- condor-tpv
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/.*:
params:
singularity_enabled: true
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/.*:
cores: 24
mem: 250
scheduling:
prefer:
- condor-tpv
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
rules:
- if: helpers.tool_version_gte(tool, '2.15.1')
# see usegalaxy-eu/issues#473: https://github.com/usegalaxy-eu/issues/issues/473
env:
_JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
- if: input_size < 0.1
cores: 1
mem: 4
- if: 0.1 <= input_size < 1
cores: 12
mem: 92
- if: 1 <= input_size < 4
cores: 16
mem: 128
- if: 4 <= input_size < 8
cores: 20
mem: 190
- if: input_size >= 80
fail: |
Too much data, we cannot support such large Trinity assemblies with our
backend. Please use another server for your job.
'.*mothur_.*':
cores: 1
mem: 90
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,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_default_container_id: centos:8.3.2011
scheduling:
require:
- docker
# see https://github.com/galaxyproject/galaxy/issues/16121#issuecomment-1555153421
##- embedded-pulsar
'.*mothur_classify_seqs.*':
cores: 2
mem: 20
params:
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_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/dnb-ds03/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:
- docker
# see https://github.com/galaxyproject/galaxy/issues/16121#issuecomment-1555153421
##- embedded-pulsar
'.*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,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_default_container_id: centos:8.3.2011
scheduling:
require:
- docker
- embedded-pulsar
'last_*':
params:
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_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/dnb-ds03/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:
- docker
- embedded-pulsar
toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/.*:
cores: 8
mem: 20
inherits: basic_docker_tool
params:
docker_run_extra_arguments: --user 999
# 4GB is enough for most of the runs as it seems
toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/.*:
cores: 1
mem: 6
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/.*:
cores: 8
mem: 20
inherits: basic_docker_tool
params:
docker_run_extra_arguments: --user 999
env:
_JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/diamond/.*:
cores: 6
mem: 90
rules:
- if: input_size >= 30
cores: 12
toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/.*:
scheduling:
require:
- docker
toolshed.g2.bx.psu.edu/repos/bgruening/openduck_run_smd/openduck_run_smd/.*:
env:
docker_set_user: 1000
docker_run_extra_arguments: '-e "OPENDUCK_GPU_PARAM=$OPENDUCK_GPU_PARAM" --gpus all'
scheduling:
require:
- docker
toolshed.g2.bx.psu.edu/repos/bgruening-util/stress_ng/stress_ng/.*:
scheduling:
require:
- singularity
- conda
toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/.*:
scheduling:
require:
- singularity
toolshed.g2.bx.psu.edu/repos/iuc/lumpy_prep/lumpy_prep/.*:
scheduling:
require:
- singularity
- conda
# is there a way to avoid this
".*pcgr.*":
mem: 16
cores: 8
env:
GALAXY_PCGR_DIR: "/data/db/databases/pcgr"
scheduling:
require:
- docker
toolshed.g2.bx.psu.edu/repos/iuc/vardict_java/vardict_java/.*:
scheduling:
require:
- singularity
- conda
# Not for Pulsar, or is the file copied?
toolshed.g2.bx.psu.edu/repos/climate/cds_essential_variability/cds_essential_variability/.*:
env:
COPERNICUS_CDSAPIRC_KEY_FILE: /data/db/data_managers/COPERNICUS_CDSAPIRC_KEY_FILE
toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/.*:
scheduling:
require:
- singularity
- conda
toolshed.g2.bx.psu.edu/repos/imgteam/overlay_moving_and_fixed_image/ip_viz_overlay_moving_and_fixed_image/.*:
cores: 8
basic_numba_tool:
env:
NUMBA_CACHE_DIR: /data/2/galaxy_db/tmp
OMP_NUM_THREADS: 4
OPENBLAS_NUM_THREADS: 4
MKL_NUM_THREADS: 4
VECLIB_MAXIMUM_THREADS: 4
NUMEXPR_NUM_THREADS: 4
NUMBA_NUM_THREADS: 4
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_process_scans/dimspy_process_scans/.*:
inherits: basic_numba_tool
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_replicate_filter/dimspy_replicate_filter/.*:
inherits: basic_numba_tool
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_align_samples/dimspy_align_samples/.*:
inherits: basic_numba_tool
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp