/
tools.yml
2560 lines (2560 loc) · 83 KB
/
tools.yml
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tools:
default:
cores: 1
mem: cores * 3.8
env: {}
params: {}
scheduling:
reject:
- offline
rules: []
rank: |
helpers.weighted_random_sampling(candidate_destinations)
testtoolshed.g2.bx.psu.edu/repos/jchung/generate_count_matrix/generate_count_matrix/.*:
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mem: 60.8
testtoolshed.g2.bx.psu.edu/repos/simon-gladman/phyloseq_ordination_plot/phyloseq_ordinate/.*:
mem: 60.8
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mem: 40
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mem: 20
toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*:
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toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/.*:
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toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/.*:
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mem: 92
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/.*:
cores: 10
mem: 90
env:
_JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
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mem: 30
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/.*:
mem: 12
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mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/.*:
cores: 24
mem: 250
scheduling:
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mem: 30
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mem: 30
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mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/.*:
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mem: 92
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mem: 160
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mem: 12
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cores: 10
mem: 90
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCoverage/.*:
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mem: 48
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mem: 12
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mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bigwigCorrelate/.*:
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeGCBias/.*:
cores: 10
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/.*:
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mem: 90
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_correctGCBias/.*:
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mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/.*:
mem: 25
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_profiler/.*:
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/.*:
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mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/.*:
cores: 10
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/.*:
cores: 10
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/.*:
cores: 10
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/.*:
cores: 10
mem: 30
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/.*:
cores: 10
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/.*:
cores: 10
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/.*:
cores: 10
mem: 40
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/.*:
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/.*:
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/.*:
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/.*:
mem: 25
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/.*:
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/.*:
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/.*:
cores: 6
mem: 90
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/.*:
cores: 10
mem: 40
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/get_online_data/ctb_online_data_fetch/.*:
mem: 10
toolshed.g2.bx.psu.edu/repos/bgruening/get_pubchem/ctb_pubchem_download_as_smiles/.*:
cores: 10
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicaggregatestatistic/hicexplorer_chicaggregatestatistic/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicdifferentialtest/hicexplorer_chicdifferentialtest/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicplotviewpoint/hicexplorer_chicplotviewpoint/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicqualitycontrol/hicexplorer_chicqualitycontrol/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicsignificantinteractions/hicexplorer_chicsignificantinteractions/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpoint/hicexplorer_chicviewpoint/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_chicviewpointbackgroundmodel/hicexplorer_chicviewpointbackgroundmodel/.*:
cores: 20
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaggregatecontacts/hicexplorer_hicaggregatecontacts/.*:
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/.*:
cores: 10
mem: 160
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/.*:
mem: 64
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrelate/hicexplorer_hiccorrelate/.*:
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/.*:
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/.*:
mem: 80
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/.*:
cores: 10
mem: 150
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/.*:
mem: 64
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/.*:
mem: 64
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/.*:
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/.*:
mem: 64
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hictransform/hicexplorer_hictransform/.*:
cores: 10
mem: 60
toolshed.g2.bx.psu.edu/repos/bgruening/hicup_mapper/hicup_mapper/.*:
cores: 6
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/.*:
cores: 20
mem: 120
rules:
- id: hifiasm_small_input_rule
if: input_size <= 0.2
cores: 6
mem: 40
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/.*:
cores: 10
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/.*:
cores: 10
mem: 20
toolshed.g2.bx.psu.edu/repos/bgruening/instagraal/instagraal/.*:
gpus: 1
cores: 1
mem: 30
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/.*:
cores: 8
mem: 40
toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/.*:
cores: 4
env:
CUDA_VISIBLE_DEVICES: 0
toolshed.g2.bx.psu.edu/repos/bgruening/minced/minced/.*:
mem: 10
toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/.*:
cores: 8
mem: 16
scheduling:
require:
- docker
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_eventalign/nanopolish_eventalign/.*:
cores: 5
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_methylation/nanopolish_methylation/.*:
cores: 5
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_polya/nanopolish_polya/.*:
cores: 3
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/.*:
cores: 5
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/.*:
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/numeric_clustering/numeric_clustering/.*:
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/openduck_run_smd/openduck_run_smd/.*:
gpus: 1
cores: 1
env:
CUDA_VISIBLE_DEVICES: 0
OPENDUCK_GPU_PARAM: --gpu-id 1
toolshed.g2.bx.psu.edu/repos/bgruening/openmg/ctb_openmg/.*:
mem: 20
env:
_JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/.*:
mem: 4
env:
_JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
scheduling:
require:
- docker
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/.*:
cores: 1
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/.*:
mem: 8
toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/.*:
cores: 16
mem: 36
toolshed.g2.bx.psu.edu/repos/bgruening/rdock_sort_filter/rdock_sort_filter/.*:
mem: 90
toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/.*:
cores: 8
mem: 40
toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_sort_filter/rxdock_sort_filter/.*:
mem: 90
toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/.*:
cores: 6
mem: 70
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/.*:
cores: 6
mem: 70
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_model_validation/sklearn_model_validation/.*:
cores: 10
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/.*:
cores: 10
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/.*:
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/.*:
mem: 8
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/.*:
mem: 12
toolshed.g2.bx.psu.edu/repos/bgruening/tgsgapcloser/tgsgapcloser/.*:
cores: 16
mem: 24
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/.*:
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