tools.yml.j2

---
# 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
    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/hifiasm/hifiasm/.*:
    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/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

  toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/.*:
    cores: 12
    mem: 40

  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')
        params:
          singularity_run_extra_arguments: "--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=False"
    scheduling:
      require:
        - singularity


  basic_docker_tool:
    scheduling:
      require:
        - docker
  toolshed.g2.bx.psu.edu/repos/bgruening/instagraal/instagraal/.*:
    inherits: basic_docker_tool
  cb_ivr:
    inherits: basic_docker_tool
  basic_illumination:
    inherits: basic_docker_tool
  mesmer:
    inherits: basic_docker_tool
  quantification:
    inherits: basic_docker_tool
  s3segmenter:
    inherits: basic_docker_tool
  unet_coreograph:
    inherits: basic_docker_tool
  unmicst:
    inherits: basic_docker_tool
  ashlar:
    inherits: basic_docker_tool
  qiime2__alignment__mafft:
    inherits: basic_docker_tool
  qiime2__alignment__mafft_add:
    inherits: basic_docker_tool
  qiime2__alignment__mask:
    inherits: basic_docker_tool
  qiime2__composition__add_pseudocount:
    inherits: basic_docker_tool
  qiime2__composition__ancom:
    inherits: basic_docker_tool
  qiime2__composition__ancombc:
    inherits: basic_docker_tool
  qiime2__composition__tabulate:
    inherits: basic_docker_tool
  qiime2__cutadapt__demux_paired:
    inherits: basic_docker_tool
  qiime2__cutadapt__demux_single:
    inherits: basic_docker_tool
  qiime2__cutadapt__trim_paired:
    inherits: basic_docker_tool
  qiime2__cutadapt__trim_single:
    inherits: basic_docker_tool
  qiime2__dada2__denoise_ccs:
    inherits: basic_docker_tool
  qiime2__dada2__denoise_paired:
    inherits: basic_docker_tool
  qiime2__dada2__denoise_pyro:
    inherits: basic_docker_tool
  qiime2__dada2__denoise_single:
    inherits: basic_docker_tool
  qiime2__deblur__denoise_16S:
    inherits: basic_docker_tool
  qiime2__deblur__denoise_other:
    inherits: basic_docker_tool
  qiime2__deblur__visualize_stats:
    inherits: basic_docker_tool
  qiime2__demux__emp_paired:
    inherits: basic_docker_tool
  qiime2__demux__emp_single:
    inherits: basic_docker_tool
  qiime2__demux__filter_samples:
    inherits: basic_docker_tool
  qiime2__demux__subsample_paired:
    inherits: basic_docker_tool
  qiime2__demux__subsample_single:
    inherits: basic_docker_tool
  qiime2__demux__summarize:
    inherits: basic_docker_tool
  qiime2__diversity__adonis:
    inherits: basic_docker_tool
  qiime2__diversity__alpha:
    inherits: basic_docker_tool
  qiime2__diversity__alpha_correlation:
    inherits: basic_docker_tool
  qiime2__diversity__alpha_group_significance:
    inherits: basic_docker_tool
  qiime2__diversity__alpha_phylogenetic:
    inherits: basic_docker_tool
  qiime2__diversity__alpha_rarefaction:
    inherits: basic_docker_tool
  qiime2__diversity__beta:
    inherits: basic_docker_tool
  qiime2__diversity__beta_correlation:
    inherits: basic_docker_tool
  qiime2__diversity__beta_group_significance:
    inherits: basic_docker_tool
  qiime2__diversity__beta_phylogenetic:
    inherits: basic_docker_tool
  qiime2__diversity__beta_rarefaction:
    inherits: basic_docker_tool
  qiime2__diversity__bioenv:
    inherits: basic_docker_tool
  qiime2__diversity__core_metrics:
    inherits: basic_docker_tool
  qiime2__diversity__core_metrics_phylogenetic:
    inherits: basic_docker_tool
  qiime2__diversity__filter_distance_matrix:
    inherits: basic_docker_tool
  qiime2__diversity__mantel:
    inherits: basic_docker_tool
  qiime2__diversity__pcoa:
    inherits: basic_docker_tool
  qiime2__diversity__pcoa_biplot:
    inherits: basic_docker_tool
  qiime2__diversity__procrustes_analysis:
    inherits: basic_docker_tool
  qiime2__diversity__tsne:
    inherits: basic_docker_tool
  qiime2__diversity__umap:
    inherits: basic_docker_tool
  qiime2__diversity_lib__alpha_passthrough:
    inherits: basic_docker_tool
  qiime2__diversity_lib__beta_passthrough:
    inherits: basic_docker_tool
  qiime2__diversity_lib__beta_phylogenetic_meta_passthrough:
    inherits: basic_docker_tool
  qiime2__diversity_lib__beta_phylogenetic_passthrough:
    inherits: basic_docker_tool
  qiime2__diversity_lib__bray_curtis:
    inherits: basic_docker_tool
  qiime2__diversity_lib__faith_pd:
    inherits: basic_docker_tool
  qiime2__diversity_lib__jaccard:
    inherits: basic_docker_tool
  qiime2__diversity_lib__observed_features:
    inherits: basic_docker_tool
  qiime2__diversity_lib__pielou_evenness:
    inherits: basic_docker_tool
  qiime2__diversity_lib__shannon_entropy:
    inherits: basic_docker_tool
  qiime2__diversity_lib__unweighted_unifrac:
    inherits: basic_docker_tool
  qiime2__diversity_lib__weighted_unifrac:
    inherits: basic_docker_tool
  qiime2__emperor__biplot:
    inherits: basic_docker_tool
  qiime2__emperor__plot:
    inherits: basic_docker_tool
  qiime2__emperor__procrustes_plot:
    inherits: basic_docker_tool
  qiime2__feature_classifier__blast:
    inherits: basic_docker_tool
  qiime2__feature_classifier__classify_consensus_blast:
    inherits: basic_docker_tool
  qiime2__feature_classifier__classify_consensus_vsearch:
    inherits: basic_docker_tool
  qiime2__feature_classifier__classify_hybrid_vsearch_sklearn:
    inherits: basic_docker_tool
  qiime2__feature_classifier__classify_sklearn:
    inherits: basic_docker_tool
  qiime2__feature_classifier__extract_reads:
    inherits: basic_docker_tool
  qiime2__feature_classifier__find_consensus_annotation:
    inherits: basic_docker_tool
  qiime2__feature_classifier__fit_classifier_naive_bayes:
    inherits: basic_docker_tool
  qiime2__feature_classifier__fit_classifier_sklearn:
    inherits: basic_docker_tool
  qiime2__feature_classifier__vsearch_global:
    inherits: basic_docker_tool
  qiime2__feature_table__core_features:
    inherits: basic_docker_tool
  qiime2__feature_table__filter_features:
    inherits: basic_docker_tool
  qiime2__feature_table__filter_features_conditionally:
    inherits: basic_docker_tool
  qiime2__feature_table__filter_samples:
    inherits: basic_docker_tool
  qiime2__feature_table__filter_seqs:
    inherits: basic_docker_tool
  qiime2__feature_table__group:
    inherits: basic_docker_tool
  qiime2__feature_table__heatmap:
    inherits: basic_docker_tool
  qiime2__feature_table__merge:
    inherits: basic_docker_tool
  qiime2__feature_table__merge_seqs:
    inherits: basic_docker_tool
  qiime2__feature_table__merge_taxa:
    inherits: basic_docker_tool
  qiime2__feature_table__presence_absence:
    inherits: basic_docker_tool
  qiime2__feature_table__rarefy:
    inherits: basic_docker_tool
  qiime2__feature_table__relative_frequency:
    inherits: basic_docker_tool
  qiime2__feature_table__rename_ids:
    inherits: basic_docker_tool
  qiime2__feature_table__subsample:
    inherits: basic_docker_tool
  qiime2__feature_table__summarize:
    inherits: basic_docker_tool
  qiime2__feature_table__tabulate_seqs:
    inherits: basic_docker_tool
  qiime2__feature_table__transpose:
    inherits: basic_docker_tool
  qiime2__fragment_insertion__classify_otus_experimental:
    inherits: basic_docker_tool
  qiime2__fragment_insertion__filter_features:
    inherits: basic_docker_tool
  qiime2__fragment_insertion__sepp:
    inherits: basic_docker_tool
  qiime2__gneiss__assign_ids:
    inherits: basic_docker_tool
  qiime2__gneiss__correlation_clustering:
    inherits: basic_docker_tool
  qiime2__gneiss__dendrogram_heatmap:
    inherits: basic_docker_tool
  qiime2__gneiss__gradient_clustering:
    inherits: basic_docker_tool
  qiime2__gneiss__ilr_hierarchical:
    inherits: basic_docker_tool
  qiime2__gneiss__ilr_phylogenetic:
    inherits: basic_docker_tool
  qiime2__gneiss__ilr_phylogenetic_differential:
    inherits: basic_docker_tool
  qiime2__gneiss__ilr_phylogenetic_ordination:
    inherits: basic_docker_tool
  qiime2__longitudinal__anova:
    inherits: basic_docker_tool
  qiime2__longitudinal__feature_volatility:
    inherits: basic_docker_tool
  qiime2__longitudinal__first_differences:
    inherits: basic_docker_tool
  qiime2__longitudinal__first_distances:
    inherits: basic_docker_tool
  qiime2__longitudinal__linear_mixed_effects:
    inherits: basic_docker_tool
  qiime2__longitudinal__maturity_index:
    inherits: basic_docker_tool
  qiime2__longitudinal__nmit:
    inherits: basic_docker_tool
  qiime2__longitudinal__pairwise_differences:
    inherits: basic_docker_tool
  qiime2__longitudinal__pairwise_distances:
    inherits: basic_docker_tool
  qiime2__longitudinal__plot_feature_volatility:
    inherits: basic_docker_tool
  qiime2__longitudinal__volatility:
    inherits: basic_docker_tool
  qiime2__metadata__distance_matrix:
    inherits: basic_docker_tool
  qiime2__metadata__shuffle_groups:
    inherits: basic_docker_tool
  qiime2__metadata__tabulate:
    inherits: basic_docker_tool
  qiime2__phylogeny__align_to_tree_mafft_fasttree:
    inherits: basic_docker_tool
  qiime2__phylogeny__align_to_tree_mafft_iqtree:
    inherits: basic_docker_tool
  qiime2__phylogeny__align_to_tree_mafft_raxml:
    inherits: basic_docker_tool
  qiime2__phylogeny__fasttree:
    inherits: basic_docker_tool
  qiime2__phylogeny__filter_table:
    inherits: basic_docker_tool
  qiime2__phylogeny__filter_tree:
    inherits: basic_docker_tool
  qiime2__phylogeny__iqtree:
    inherits: basic_docker_tool
  qiime2__phylogeny__iqtree_ultrafast_bootstrap:
    inherits: basic_docker_tool
  qiime2__phylogeny__midpoint_root:
    inherits: basic_docker_tool
  qiime2__phylogeny__raxml:
    inherits: basic_docker_tool
  qiime2__phylogeny__raxml_rapid_bootstrap:
    inherits: basic_docker_tool
  qiime2__phylogeny__robinson_foulds:
    inherits: basic_docker_tool
  qiime2__quality_control__bowtie2_build:
    inherits: basic_docker_tool
  qiime2__quality_control__evaluate_composition:
    inherits: basic_docker_tool
  qiime2__quality_control__evaluate_seqs:
    inherits: basic_docker_tool
  qiime2__quality_control__evaluate_taxonomy:
    inherits: basic_docker_tool
  qiime2__quality_control__exclude_seqs:
    inherits: basic_docker_tool
  qiime2__quality_control__filter_reads:
    inherits: basic_docker_tool
  qiime2__quality_filter__q_score:
    inherits: basic_docker_tool
  qiime2__sample_classifier__classify_samples:
    inherits: basic_docker_tool
  qiime2__sample_classifier__classify_samples_from_dist:
    inherits: basic_docker_tool
  qiime2__sample_classifier__classify_samples_ncv:
    inherits: basic_docker_tool
  qiime2__sample_classifier__confusion_matrix:
    inherits: basic_docker_tool
  qiime2__sample_classifier__fit_classifier:
    inherits: basic_docker_tool
  qiime2__sample_classifier__fit_regressor:
    inherits: basic_docker_tool
  qiime2__sample_classifier__heatmap:
    inherits: basic_docker_tool
  qiime2__sample_classifier__metatable:
    inherits: basic_docker_tool
  qiime2__sample_classifier__predict_classification:
    inherits: basic_docker_tool
  qiime2__sample_classifier__predict_regression:
    inherits: basic_docker_tool
  qiime2__sample_classifier__regress_samples:
    inherits: basic_docker_tool
  qiime2__sample_classifier__regress_samples_ncv:
    inherits: basic_docker_tool
  qiime2__sample_classifier__scatterplot:
    inherits: basic_docker_tool
  qiime2__sample_classifier__split_table:
    inherits: basic_docker_tool
  qiime2__sample_classifier__summarize:
    inherits: basic_docker_tool
  qiime2__taxa__barplot:
    inherits: basic_docker_tool
  qiime2__taxa__collapse:
    inherits: basic_docker_tool
  qiime2__taxa__filter_seqs:
    inherits: basic_docker_tool
  qiime2__taxa__filter_table:
    inherits: basic_docker_tool
  qiime2__vsearch__cluster_features_closed_reference:
    inherits: basic_docker_tool
  qiime2__vsearch__cluster_features_de_novo:
    inherits: basic_docker_tool
  qiime2__vsearch__cluster_features_open_reference:
    inherits: basic_docker_tool
  qiime2__vsearch__dereplicate_sequences:
    inherits: basic_docker_tool
  qiime2__vsearch__fastq_stats:
    inherits: basic_docker_tool
  qiime2__vsearch__merge_pairs:
    inherits: basic_docker_tool
  qiime2__vsearch__uchime_denovo:
    inherits: basic_docker_tool
  qiime2__vsearch__uchime_ref:
    inherits: basic_docker_tool
  qiime2_core__tools__export:
    inherits: basic_docker_tool
  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/iuc/cherri_eval/cherri_eval/.*:
    inherits: basic_docker_tool
    cores: 1
    mem: 20

  toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/.*:
    cores: 2
    mem: 70

  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/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: 8
    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: 0.1 <= input_size < 1
        cores: 20
        mem: 100
      - if: 1 <= input_size < 2
        cores: 30
        mem: 200
      - if: 2 <= input_size < 30
        cores: 60
        mem: 950
      - if: input_size >= 30
        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:
      submit_requirements: 'GalaxyGroup == "compute_mothur"'
      docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
      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:
      submit_requirements: 'GalaxyGroup == "compute_mothur"'
      docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
      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_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_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
  toolshed.g2.bx.psu.edu/repos/iracooke/msgfplus/msgfplus/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
  toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/.*:
    rules:
      - if: helpers.tool_version_lt(tool, '4.1.5')
        env:
          RM_LIB_PATH: "/data/db/databases/dfam/3.4/"
      - if: helpers.tool_version_gte(tool, '4.1.5')
        cores: 4
  toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx17G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/iuc/bbtools_callvariants/bbtools_callvariants/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/.*:
    env:
      _JAVA_OPTIONS: -Xmx4G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=4G -Xmx120G -Xms4G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=6G -Xmx14G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/.*:
    inherits: basic_numba_tool

  toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/.*:
    inherits: basic_numba_tool

  toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/.*:
    inherits: basic_numba_tool

  toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/.*:
    inherits: basic_numba_tool

  toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/.*:
    inherits: basic_numba_tool

  toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/.*:
    inherits: basic_numba_tool

  toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/.*:
    env:
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/.*:
    cores: 16
    mem: 90
    env:
      TERM: vt100
      _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp

  toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/.*:
    scheduling:
      require:
        - singularity

  # Also on add_to_tpv_shared_db.yml but without NUMBA_CACHE_DIR
  toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/.*:
    inherits: basic_numba_tool

  toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/.*:
    scheduling:
      require:
        - singularity
        - conda

  toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/.*:
    scheduling:
      require:
        - singularity
        - conda

  toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/.*:
    scheduling:
      require:
        - singularity
        - conda

  toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/.*:
    scheduling:
      require:
        - singularity
        - conda

  toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/.*:
    mem: 8

  toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/.*:
    scheduling:
      require:
        - singularity

  ".*srma_wrapper.*":
    scheduling:
      require:
        - singularity
    params:
      singularity_default_container_id: "{{ cvmfs.singularity.path }}/all/python:2.7.16"