Permalink
Cannot retrieve contributors at this time
1115 lines (1066 sloc)
36.5 KB
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| __default__: {} | |
| keras_train_and_eval: | |
| runner: remote_condor_cluster_gpu | |
| gpus: 1 | |
| cores: 10 | |
| env: | |
| CUDA_VISIBLE_DEVICES: 0 | |
| xchem_transfs_scoring: | |
| runner: remote_condor_cluster_gpu_docker | |
| gpus: 1 | |
| cores: 1 | |
| env: | |
| CUDA_VISIBLE_DEVICES: 0 | |
| xchem_pose_scoring: | |
| runner: remote_condor_cluster_gpu_docker | |
| gpus: 1 | |
| cores: 1 | |
| env: | |
| CUDA_VISIBLE_DEVICES: 0 | |
| openduck_run_smd: | |
| runner: remote_condor_cluster_gpu_docker | |
| gpus: 1 | |
| cores: 1 | |
| env: | |
| CUDA_VISIBLE_DEVICES: 0 | |
| OPENDUCK_GPU_PARAM: "--gpu-id 1" | |
| docker_set_user: 1000 | |
| docker_run_extra_arguments: '-e "OPENDUCK_GPU_PARAM=$OPENDUCK_GPU_PARAM" --gpus all' | |
| sklearn_searchcv: {mem: 12, cores: 10} | |
| sklearn_model_validation: {mem: 12, cores: 10} | |
| # These are interactive and get restricted volumes | |
| interactive_tool_jupyter_notebook: | |
| mem: 4 | |
| runner: condor_docker_ie_interactive | |
| env: | |
| HOME: /home/jovyan | |
| force_destination_id: True | |
| interactive_tool_climate_notebook: | |
| mem: 4 | |
| runner: condor_docker_ie_interactive | |
| env: | |
| HOME: /home/jovyan | |
| force_destination_id: True | |
| interactive_ml_tool_jupyter_notebook: | |
| ##runner: remote_condor_cluster_gpu_docker | |
| runner: condor_docker_ie_interactive | |
| force_destination_id: True | |
| ##gpus: 1 | |
| cores: 1 | |
| mem: 8 | |
| env: | |
| CUDA_VISIBLE_DEVICES: 0 | |
| ##docker_set_user: 1000 | |
| ##docker_run_extra_arguments: ' --gpus all ' | |
| interactive_tool_rstudio: {mem: 8, cores: 1, runner: condor_docker_ie_interactive, force_destination_id: True} | |
| interactive_tool_pyiron: {mem: 8, cores: 1, runner: condor_docker_ie_interactive, force_destination_id: True} | |
| interactive_tool_guacamole_desktop: {mem: 8, cores: 2, runner: condor_docker_ie_interactive, force_destination_id: True} | |
| interactive_tool_openrefine: {mem: 4, runner: condor_docker_ie_interactive, force_destination_id: True} | |
| interactive_tool_panoply: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_vrm_editor: {mem: 4, cores: 1, runner: condor_docker_ie_interactive, force_destination_id: True} | |
| # These are not | |
| interactive_tool_ethercalc: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_geoexplorer: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_radiant: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_higlass: {mem: 20, cores: 5, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_phinch: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_neo4j: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_hicbrowser: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_cellxgene: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_bam_iobio: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_vcf_iobio: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_askomics: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_wilson: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_wallace: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_paraview: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| interactive_tool_simtext_app: {mem: 4, runner: condor_docker_ie, force_destination_id: True} | |
| transdecoder: {cores: 8, mem: 8} | |
| zerone: {runner: remote_cluster_mq_it01} | |
| basil: {runner: remote_cluster_mq_it01} | |
| #goenrichment: {runner: remote_cluster_mq_be01} | |
| circos: {mem: 10, runner: remote_cluster_mq_pt01} | |
| # docking: {runner: remote_cluster_mq_uk01} | |
| # prepare_ligands_for_docking: {runner: remote_cluster_mq_it01} | |
| # prepare_box: {runner: remote_cluster_mq_uk01} | |
| stress_ng: {runner: condor_singularity_with_conda} | |
| fasterq_dump: {cores: 8} | |
| busco: {cores: 16, mem: 80} | |
| # roary needs many many cpus if the number of input files increase | |
| # a more specific function would ne neat | |
| roary: {cores: 24} | |
| alevin: {mem: 92, cores: 8} | |
| kc-align: {cores: 3} | |
| maxquant: {mem: 60, cores: 8} | |
| scpipe: {mem: 64, cores: 8} | |
| cardinal_combine: {mem: 92} | |
| cardinal_classification: {mem: 100} | |
| cardinal_filtering: {mem: 60} | |
| cardinal_mz_images: {mem: 20} | |
| cardinal_preprocessing: {cores: 4, mem: 110} | |
| cardinal_quality_report: {mem: 180} | |
| cardinal_segmentations: {mem: 92} | |
| cardinal_spectra_plots: {mem: 32} | |
| cardinal_data_exporter: {mem: 200} | |
| kraken_database_builder: {mem: 200} | |
| heatmap: {mem: 12} | |
| Heatmap: {mem: 12} | |
| msconvert: {runner: condor_docker} | |
| bionano_scaffold: | |
| runner: condor_docker | |
| mem: 256 | |
| cores: 24 | |
| RNAlien: {cores: 10} | |
| slamdunk: {cores: 10} | |
| tombo_resquiggle: {cores: 10, mem: 32} | |
| tombo_detect_modifications: {cores: 10, mem: 32} | |
| pangolin: {cores: 8} | |
| pilon: | |
| mem: 32 | |
| env: | |
| _JAVA_OPTIONS: -Xmx32G -Xms1G | |
| encyclopedia_prosit_csv_to_library: | |
| mem: 40 | |
| env: | |
| _JAVA_OPTIONS: -Xmx40G -Xms1G | |
| vardict_java: | |
| runner: condor_singularity_with_conda | |
| mem: 512 | |
| cores: 2 | |
| env: | |
| _JAVA_OPTIONS: -Xmx512G -Xms1G | |
| paralyzer: | |
| mem: 8 | |
| env: | |
| _JAVA_OPTIONS: -Xmx8G -Xms1G | |
| cuffmerge: {mem: 8} | |
| CruxAdapter: {mem: 8} | |
| bio3d_pca: {mem: 64} | |
| bio3d_rmsd: {mem: 100} | |
| bio3d_rmsf: {mem: 100} | |
| rxdock_sort_filter: {mem: 100} | |
| rdock_sort_filter: {mem: 100} | |
| cds_essential_variability: | |
| env: | |
| COPERNICUS_CDSAPIRC_KEY_FILE: /data/db/data_managers/COPERNICUS_CDSAPIRC_KEY_FILE | |
| idr_download_by_ids: {mem: 24, runner: condor_singularity_with_conda} | |
| kraken: {mem: 100} | |
| kraken2: {mem: 64} | |
| ont_fast5_api_compress_fast5: {cores: 8} | |
| viz_overlay_moving_and_fixed_image: {mem: 12} | |
| ip_projective_transformation: {mem: 24} | |
| scale_image: {mem: 12} | |
| re_he_maldi_image_registration: {mem: 48} | |
| minimap2: {cores: 8, mem: 32} | |
| winnowmap: {cores: 8, mem: 32} | |
| flye: {cores: 20, mem: 24} | |
| msstats: {mem: 24} | |
| msstatstmt: {mem: 24} | |
| dimspy_process_scans: | |
| cores: 4 | |
| mem: 12 | |
| 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 | |
| dimspy_replicate_filter: | |
| cores: 4 | |
| mem: 12 | |
| 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 | |
| dimspy_align_samples: | |
| cores: 4 | |
| mem: 12 | |
| 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 | |
| dimspy_blank_filter: {mem: 12} | |
| dimspy_sample_filter: {mem: 12} | |
| dimspy_missing_values_sample_filter: {mem: 12} | |
| nanopolish_methylation: {cores: 5, mem: 12} | |
| nanopolish_variants: {cores: 5, mem: 12} | |
| nanopolish_eventalign: {cores: 5, mem: 12} | |
| nanopolishcomp_eventaligncollapse: {cores: 10, mem: 12} | |
| nanocompore_sampcomp: {cores: 9, mem: 48} | |
| AccurateMassSearch: {cores: 4, mem: 8} | |
| AdditiveSeries: {cores: 20, mem: 12} | |
| # augustus: {runner: remote_cluster_mq_be01} | |
| BaselineFilter: {cores: 4, mem: 8} | |
| CONVERTER_bedgraph_to_bigwig: {mem: 8} | |
| CVInspector: {cores: 4, mem: 8} | |
| CompNovo: {cores: 4, mem: 8} | |
| CompNovoCID: {cores: 4, mem: 8} | |
| ConsensusID: {cores: 1, mem: 58} | |
| ConsensusMapNormalizer: {cores: 4, mem: 8} | |
| DeMeanderize: {cores: 4, mem: 8} | |
| Decharger: {cores: 4, mem: 8} | |
| DecoyDatabase: {cores: 4, mem: 8} | |
| Digestor: {cores: 4, mem: 8} | |
| DigestorMotif: {cores: 4, mem: 8} | |
| EICExtractor: {cores: 4, mem: 8} | |
| 'EMBOSS: fuzztran39': {mem: 10} | |
| ERPairFinder: {cores: 4, mem: 8} | |
| FFEval: {cores: 4, mem: 8} | |
| FalseDiscoveryRate: {cores: 4, mem: 8} | |
| FeatureFinderCentroided: {cores: 4, mem: 8} | |
| FeatureFinderIsotopeWavelet: {cores: 4, mem: 8} | |
| FeatureFinderMRM: {cores: 4, mem: 8} | |
| FeatureFinderMetabo: {cores: 4, mem: 8} | |
| FeatureFinderMultiplex: {cores: 8, mem: 8} | |
| FeatureFinderSuperHirn: {cores: 4, mem: 8} | |
| FeatureLinkerLabeled: {cores: 4, mem: 8} | |
| FeatureLinkerUnlabeled: {cores: 4, mem: 8} | |
| FeatureLinkerUnlabeledQT: {cores: 4, mem: 8} | |
| FidoAdapter: {cores: 8, mem: 8} | |
| FileConverter: {cores: 4, mem: 8} | |
| FileFilter: {cores: 4, mem: 8} | |
| FileInfo: {cores: 4, mem: 8} | |
| FileMerger: {cores: 4, mem: 16} | |
| HighResPrecursorMassCorrector: {cores: 4, mem: 8} | |
| IDConflictResolver: {cores: 4, mem: 8} | |
| IDEvaluator: {cores: 4, mem: 8} | |
| IDExtractor: {cores: 4, mem: 8} | |
| IDFileConverter: {cores: 4, mem: 8} | |
| IDFilter: {cores: 4, mem: 8} | |
| IDMapper: {cores: 4, mem: 8} | |
| IDMassAccuracy: {cores: 4, mem: 8} | |
| IDMerger: {cores: 1, mem: 30} | |
| IDPosteriorErrorProbability: {cores: 4, mem: 8} | |
| IDRTCalibration: {cores: 4, mem: 8} | |
| IDSplitter: {cores: 4, mem: 8} | |
| ITRAQAnalyzer: {cores: 4, mem: 8} | |
| ImageCreator: {cores: 4, mem: 8} | |
| InclusionExclusionListCreator: {cores: 4, mem: 8} | |
| InternalCalibration: {cores: 4, mem: 8} | |
| IsobaricAnalyzer: {cores: 4, mem: 8} | |
| LabeledEval: {cores: 4, mem: 8} | |
| #maker: {cores: 8, mem: 8, runner: remote_cluster_mq_fr01} | |
| gmx_sim: {cores: 8, mem: 8, gpus: 1, runner: condor_gpu} | |
| gmx_em: {cores: 16, mem: 8} | |
| gmx_fep: {cores: 16, mem: 8} | |
| # gmx_md: {runner: remote_cluster_mq_de02} | |
| # gmx_merge_topology_files: {runner: remote_cluster_mq_de02} | |
| # gmx_em: {runner: remote_cluster_mq_de02} | |
| # gmx_nvt: {runner: remote_cluster_mq_de02} | |
| # gmx_npt: {runner: remote_cluster_mq_de02} | |
| # gmx_setup: {runner: remote_cluster_mq_de02} | |
| # gmx_solvate: {runner: remote_cluster_mq_de02} | |
| # mdanalysis_hbonds: {runner: remote_cluster_mq_de02} | |
| mdanalysis_extract_rmsd: {cores: 4, mem: 16} | |
| MRMMapper: {cores: 4, mem: 8} | |
| MRMPairFinder: {cores: 4, mem: 8} | |
| msgfplus: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp | |
| mem: 12 | |
| name: special | |
| MSGFPlusAdapter: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp | |
| mem: 12 | |
| name: special | |
| medaka_variant: {mem: 48} | |
| repeatmasker_wrapper: {cores: 8} | |
| mass_spectrometry_imaging_segmentations: {mem: 92} | |
| mass_spectrometry_imaging_combine: {mem: 12} | |
| mass_spectrometry_imaging_mzplots: {mem: 24} | |
| msi_ion_images: {mem: 92} | |
| msi_spectra_plot: {mem: 210} | |
| MSSimulator: {cores: 4, mem: 8} | |
| MapAlignerIdentification: {cores: 4, mem: 8} | |
| MapAlignerPoseClustering: {cores: 4, mem: 8} | |
| MapAlignerSpectrum: {cores: 4, mem: 8} | |
| MapAlignmentEvaluation: {cores: 4, mem: 8} | |
| MapNormalizer: {cores: 4, mem: 8} | |
| MapRTTransformer: {cores: 4, mem: 8} | |
| MapStatistics: {cores: 4, mem: 8} | |
| MassCalculator: {cores: 4, mem: 8} | |
| MassTraceExtractor: {cores: 4, mem: 8} | |
| MyriMatchAdapter: {cores: 4, mem: 8} | |
| MzTabExporter: {cores: 4, mem: 8} | |
| QCCalculator: {mem: 8} | |
| OpenSwathWorkflow: {mem: 156} | |
| mira_assembler: {mem: 24} | |
| meryl: {cores: 8, mem: 152} | |
| mothur_align_check: {cores: 8, env: {TERM: vt100}} | |
| mothur_align_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_amova: {cores: 8, env: {TERM: vt100}} | |
| mothur_anosim: {cores: 8, env: {TERM: vt100}} | |
| mothur_bin_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_chimera_bellerophon: {cores: 8, env: {TERM: vt100}} | |
| mothur_chimera_ccode: {cores: 8, env: {TERM: vt100}} | |
| mothur_chimera_check: {cores: 8, env: {TERM: vt100}} | |
| mothur_chimera_perseus: {cores: 8, env: {TERM: vt100}} | |
| mothur_chimera_pintail: {cores: 8, env: {TERM: vt100}} | |
| mothur_chimera_slayer: {cores: 8, env: {TERM: vt100}} | |
| mothur_chimera_uchime: {cores: 8, env: {TERM: vt100}} | |
| mothur_chop_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_classify_otu: {cores: 8, env: {TERM: vt100}} | |
| mothur_classify_rf: {cores: 8, env: {TERM: vt100}} | |
| mothur_classify_seqs: {cores: 8, mem: 8, env: {TERM: vt100}} | |
| mothur_classify_tree: {cores: 8, env: {TERM: vt100}} | |
| mothur_clearcut: {cores: 8, env: {TERM: vt100}} | |
| mothur_cluster: {cores: 8, env: {TERM: vt100}} | |
| mothur_cluster_classic: {cores: 8, env: {TERM: vt100}} | |
| mothur_cluster_fragments: {cores: 8, env: {TERM: vt100}} | |
| mothur_cluster_split: {cores: 8, env: {TERM: vt100}, runner: condor_singularity} | |
| mothur_collect_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_collect_single: {cores: 8, env: {TERM: vt100}} | |
| mothur_consensus_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_cooccurrence: {cores: 8, env: {TERM: vt100}} | |
| mothur_corr_axes: {cores: 8, env: {TERM: vt100}} | |
| mothur_count_groups: {cores: 8, env: {TERM: vt100}} | |
| mothur_count_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_create_database: {cores: 8, env: {TERM: vt100}} | |
| mothur_degap_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_deunique_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_deunique_tree: {cores: 8, env: {TERM: vt100}} | |
| mothur_dist_seqs: {cores: 8, env: {TERM: vt100}, runner: condor_singularity} | |
| mothur_dist_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_fastq_info: {cores: 8, env: {TERM: vt100}} | |
| mothur_filter_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_filter_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_communitytype: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_coremicrobiome: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_dists: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_group: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_groups: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_label: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_lineage: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_mimarkspackage: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_otulabels: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_otulist: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_oturep: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_otus: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_rabund: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_relabund: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_sabund: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_get_sharedseqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_hcluster: {cores: 8, env: {TERM: vt100}} | |
| mothur_heatmap_bin: {cores: 8, env: {TERM: vt100}} | |
| mothur_heatmap_sim: {cores: 8, env: {TERM: vt100}} | |
| mothur_homova: {cores: 8, env: {TERM: vt100}} | |
| mothur_indicator: {cores: 8, env: {TERM: vt100}} | |
| mothur_lefse: {cores: 8, env: {TERM: vt100}} | |
| mothur_libshuff: {cores: 8, env: {TERM: vt100}} | |
| mothur_list_otulabels: {cores: 8, env: {TERM: vt100}} | |
| mothur_list_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_biom: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_contigs: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_design: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_fastq: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_group: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_lefse: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_lookup: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_make_sra: {cores: 8, env: {TERM: vt100}} | |
| mothur_mantel: {cores: 8, env: {TERM: vt100}} | |
| mothur_merge_files: {cores: 8, env: {TERM: vt100}} | |
| mothur_merge_groups: {cores: 8, env: {TERM: vt100}} | |
| mothur_merge_sfffiles: {cores: 8, env: {TERM: vt100}} | |
| mothur_merge_taxsummary: {cores: 8, env: {TERM: vt100}} | |
| mothur_metastats: {cores: 8, env: {TERM: vt100}} | |
| mothur_mimarks_attributes: {cores: 8, env: {TERM: vt100}} | |
| mothur_nmds: {cores: 8, env: {TERM: vt100}} | |
| mothur_normalize_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_otu_association: {cores: 8, env: {TERM: vt100}} | |
| mothur_otu_hierarchy: {cores: 8, env: {TERM: vt100}} | |
| mothur_pairwise_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_parse_list: {cores: 8, env: {TERM: vt100}} | |
| mothur_parsimony: {cores: 8, env: {TERM: vt100}} | |
| mothur_pca: {cores: 8, env: {TERM: vt100}} | |
| mothur_pcoa: {cores: 8, env: {TERM: vt100}} | |
| mothur_pcr_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_phylo_diversity: {cores: 8, env: {TERM: vt100}} | |
| mothur_phylotype: {cores: 8, env: {TERM: vt100}} | |
| mothur_pre_cluster: {cores: 8, env: {TERM: vt100}} | |
| mothur_primer_design: {cores: 8, env: {TERM: vt100}} | |
| mothur_rarefaction_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_rarefaction_single: {cores: 8, env: {TERM: vt100}} | |
| mothur_remove_dists: {cores: 8, env: {TERM: vt100}} | |
| mothur_remove_groups: {cores: 8, env: {TERM: vt100}} | |
| mothur_remove_lineage: {cores: 8, env: {TERM: vt100}} | |
| mothur_remove_otulabels: {cores: 8, env: {TERM: vt100}} | |
| mothur_remove_otus: {cores: 8, env: {TERM: vt100}} | |
| mothur_remove_rare: {cores: 8, env: {TERM: vt100}} | |
| mothur_remove_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_reverse_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_screen_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_sens_spec: {cores: 8, env: {TERM: vt100}} | |
| mothur_seq_error: {cores: 8, env: {TERM: vt100}} | |
| mothur_sffinfo: {cores: 8, env: {TERM: vt100}} | |
| mothur_shhh_flows: {cores: 8, env: {TERM: vt100}} | |
| mothur_shhh_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_sort_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_split_abund: {cores: 8, env: {TERM: vt100}} | |
| mothur_split_groups: {cores: 8, env: {TERM: vt100}} | |
| mothur_sub_sample: {cores: 8, env: {TERM: vt100}} | |
| mothur_summary_qual: {cores: 8, env: {TERM: vt100}} | |
| mothur_summary_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_summary_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_summary_single: {cores: 8, env: {TERM: vt100}} | |
| mothur_summary_tax: {cores: 8, env: {TERM: vt100}} | |
| mothur_tree_shared: {cores: 8, env: {TERM: vt100}} | |
| mothur_trim_flows: {cores: 8, env: {TERM: vt100}} | |
| mothur_trim_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_unifrac_unweighted: {cores: 8, env: {TERM: vt100}} | |
| mothur_unifrac_weighted: {cores: 8, env: {TERM: vt100}} | |
| mothur_unique_seqs: {cores: 8, env: {TERM: vt100}} | |
| mothur_venn: {cores: 8, env: {TERM: vt100}} | |
| mz_to_sqlite: | |
| mem: 16 | |
| env: | |
| _JAVA_OPTIONS: -Xmx16G -Xms1G | |
| NSPDK_candidateClust: {mem: 32} | |
| NoiseFilterGaussian: {cores: 4, mem: 8} | |
| NoiseFilterSGolay: {cores: 4, mem: 8} | |
| OMSSAAdapter: {cores: 4, mem: 8} | |
| OpenSwathAnalyzer: {cores: 4, mem: 8} | |
| OpenSwathChromatogramExtractor: {cores: 4, mem: 8} | |
| OpenSwathConfidenceScoring: {cores: 4, mem: 8} | |
| OpenSwathDIAPreScoring: {cores: 4, mem: 8} | |
| OpenSwathDecoyGenerator: {cores: 4, mem: 8} | |
| OpenSwathFeatureXMLToTSV: {cores: 4, mem: 8} | |
| OpenSwathRTNormalizer: {cores: 4, mem: 8} | |
| OpenSwathRewriteToFeatureXML: {cores: 4, mem: 8} | |
| PTModel: {cores: 4, mem: 8} | |
| PTPredict: {cores: 4, mem: 8} | |
| PeakPickerHiRes: {cores: 4, mem: 8} | |
| PeakPickerWavelet: {cores: 4, mem: 8} | |
| PepNovoAdapter: {cores: 4, mem: 8} | |
| PeptideIndexer: {cores: 4, mem: 8} | |
| PicardASMetrics: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| PicardGCBiasMetrics: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| PicardHsMetrics: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| PicardInsertSize: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| picard_CleanSam: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| AssayGeneratorMetabo: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| PrecursorIonSelector: {cores: 4, mem: 8} | |
| PrecursorMassCorrector: {cores: 4, mem: 8} | |
| ProteinInference: {cores: 4, mem: 8} | |
| ProteinQuantifier: {cores: 4, mem: 8} | |
| ProteinResolver: {cores: 4, mem: 8} | |
| RNPxl: {cores: 4, mem: 8} | |
| RTEvaluation: {cores: 4, mem: 8} | |
| RTModel: {cores: 4, mem: 8} | |
| RTPredict: {cores: 4, mem: 8} | |
| Resampler: {cores: 4, mem: 8} | |
| SeedListGenerator: {cores: 4, mem: 8} | |
| SemanticValidator: {cores: 4, mem: 8} | |
| SequenceCoverageCalculator: {cores: 4, mem: 8} | |
| SpecLibCreator: {cores: 4, mem: 8} | |
| SpecLibSearcher: {cores: 4, mem: 8} | |
| SpectraFilterBernNorm: {cores: 4, mem: 8} | |
| SpectraFilterMarkerMower: {cores: 4, mem: 8} | |
| SpectraFilterNLargest: {cores: 4, mem: 8} | |
| SpectraFilterNormalizer: {cores: 4, mem: 8} | |
| SpectraFilterParentPeakMower: {cores: 4, mem: 8} | |
| SpectraFilterScaler: {cores: 4, mem: 8} | |
| SpectraFilterSqrtMower: {cores: 4, mem: 8} | |
| SpectraFilterThresholdMower: {cores: 4, mem: 8} | |
| SpectraFilterWindowMower: {cores: 4, mem: 8} | |
| SpectraMerger: {cores: 4, mem: 8} | |
| SiriusAdapter: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| TMTAnalyzer: {cores: 4, mem: 8} | |
| TOFCalibration: {cores: 4, mem: 8} | |
| TextExporter: {cores: 4, mem: 8} | |
| TransformationEvaluation: {cores: 4, mem: 8} | |
| XMLValidator: {cores: 4, mem: 8} | |
| XTandemAdapter: {cores: 4, mem: 8} | |
| racon: {cores: 4, mem: 24} | |
| abims_xcms_fillPeaks: {mem: 32} | |
| abims_xcms_retcor: {mem: 32} | |
| abims_CAMERA_annotateDiffreport: {mem: 32} | |
| anndata_export: {cores: 4} | |
| anndata_import: {cores: 4} | |
| anndata_inspect: {cores: 4} | |
| anndata_manipulate: {cores: 4} | |
| antismash: | |
| cores: 10 | |
| mem: 100 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx96G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| bam-to-wig: {mem: 20} | |
| bamCompare_deepTools: {mem: 10} | |
| bamCorrelate_deepTools: {cores: 10, mem: 100} | |
| bamCoverage_deepTools: {mem: 10} | |
| bamFingerprint: {mem: 10} | |
| bedtools_intersectbed: {mem: 40} | |
| bedtools_intersectbed_bam: {mem: 40} | |
| bedtools_mergebed: {mem: 15} | |
| bedtools_sortbed: {mem: 20} | |
| bedtools_subtractbed: {mem: 8} | |
| bfast_wrapper: {cores: 10, mem: 20} | |
| bg_diamond: {cores: 6, mem: 90} | |
| bg_diamond_makedb: {cores: 10, mem: 40} | |
| bgchem_fragment_merger: {cores: 10, mem: 40} | |
| bigwig_to_bedgraph: {mem: 12} | |
| biosigner: {mem: 12} | |
| bismark_bowtie: {cores: 6, mem: 30, name: bismark, tmp: large} | |
| bismark_bowtie2: {cores: 6, mem: 30, name: bismark, tmp: large} | |
| blast2go: {mem: 20} | |
| blast_parser: {mem: 8} | |
| blockbuster: {mem: 64} | |
| blockclust: {mem: 10} | |
| bowtie2: {cores: 8, mem: 20} | |
| bwa: {cores: 8, mem: 20} | |
| bwa_mem: {cores: 8, mem: 30} | |
| bwa_mem_index_builder_data_manager: {mem: 48} | |
| bwameth_index_builder_data_manager: {mem: 48} | |
| kallisto_index_builder_data_manager: {mem: 92} | |
| salmon_index_builder_data_manager: {mem: 92} | |
| data_manager_metaphlan_download: {cores: 12, mem: 92} | |
| bwameth: {cores: 8, mem: 24} | |
| bwtool-lift: {mem: 80} | |
| cat_contigs: {mem: 24} ## Diamond in the background | |
| cat_bins: {mem: 24} ## Diamond in the background | |
| chira_map: {cores: 10, mem: 80, runner: condor_singularity_with_conda} | |
| chira_merge: {cores: 1, mem: 60, runner: condor_singularity_with_conda} | |
| chira_quantify: {cores: 1, mem: 60, runner: condor_singularity_with_conda} | |
| chira_extract: {cores: 24, mem: 60, runner: condor_singularity_with_conda} | |
| canu: {cores: 20, mem: 92} | |
| mass_spectrometry_imaging_preprocessing: {mem: 110} | |
| mass_spectrometry_imaging_ion_images: {mem: 20} | |
| mass_spectrometry_imaging_qc: {mem: 110} | |
| mass_spectrometry_imaging_filtering: {mem: 20} | |
| metaspades: {cores: 10, mem: 250} | |
| megahit: {cores: 10, mem: 48} | |
| charts: {mem: 10} | |
| circgraph: {mem: 10} | |
| computeMatrix: {mem: 100} | |
| correctGCBias: {mem: 10} | |
| cshl_fastx_collapser: {mem: 16} | |
| create_tool_recommendation_model: {cores: 16, mem: 160} | |
| crispr_recognition_tool: {mem: 10} | |
| ctb_np-likeness-calculator: {mem: 12} | |
| ctb_online_data_fetch: {mem: 10} | |
| ctb_openmg: | |
| mem: 20 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| ctb_pubchem_download_as_smiles: {cores: 10, mem: 20} | |
| cuffcompare: {mem: 10} | |
| cuffdiff: {cores: 6, mem: 40} | |
| cufflinks: {cores: 6, mem: 30} | |
| cuffnorm: {cores: 6, mem: 20} | |
| cuffquant: {cores: 6, mem: 20} | |
| data_manager_gemini_download: {mem: 20} | |
| data_manager_humann2_download: {mem: 25} | |
| data_manager_snpeff_databases: {mem: 12} | |
| data_manager_snpeff_download: {mem: 12} | |
| deeptools_bamCompare: {cores: 10, mem: 12} | |
| deeptools_bamCorrelate: {cores: 10, mem: 90} | |
| deeptools_bamCoverage: {cores: 10, mem: 48} | |
| deeptools_bamFingerprint: {cores: 10, mem: 12} | |
| deeptools_bam_compare: {cores: 10, mem: 24} | |
| deeptools_bam_coverage: {cores: 10, mem: 24} | |
| deeptools_bam_pe_fragmentsize: {cores: 10, mem: 24} | |
| deeptools_bigwigCompare: {cores: 10, mem: 12} | |
| deeptools_bigwigCorrelate: {cores: 10, mem: 40} | |
| deeptools_bigwig_compare: {cores: 10, mem: 24} | |
| deeptools_computeGCBias: {cores: 10, mem: 24} | |
| deeptools_computeMatrix: {cores: 10, mem: 40} | |
| deeptools_compute_gc_bias: {cores: 10, mem: 24} | |
| deeptools_compute_matrix: {cores: 10, mem: 30} | |
| deeptools_correctGCBias: {cores: 10, mem: 24} | |
| deeptools_correct_gc_bias: {cores: 10, mem: 24} | |
| deeptools_heatmapper: {mem: 25} | |
| deeptools_multi_bam_summary: {cores: 10, mem: 24} | |
| deeptools_multi_bigwig_summary: {cores: 10, mem: 40} | |
| deeptools_plot_correlation: {mem: 20} | |
| deeptools_plot_coverage: {mem: 20} | |
| deeptools_plot_fingerprint: {mem: 20} | |
| deeptools_plot_heatmap: {mem: 25} | |
| deeptools_plot_pca: {mem: 20} | |
| deeptools_plot_profile: {mem: 20} | |
| deeptools_profiler: {mem: 20} | |
| deseq2: {mem: 8} | |
| dexseq_count: {mem: 25} | |
| diamond_database_builder: {cores: 10, mem: 90} | |
| dt_profiler: {mem: 10} | |
| eukaryotic_ncbi_submission: {cores: 24, mem: 24} | |
| fastq_dump: {mem: 20} | |
| fastqc: {mem: 20} | |
| featurecounts: {cores: 8, mem: 18} | |
| feebayes: {cores: 10, mem: 12} | |
| flashlfq: | |
| env: | |
| MONO_GC_PARAMS: max-heap-size=90g | |
| mem: 90 | |
| flexbar: {cores: 10, mem: 12} | |
| flexbar_no_split: {cores: 10, mem: 12} | |
| flexbar_split_RR_bcs: {cores: 10, mem: 12} | |
| flexbar_split_RYYR_bcs: {cores: 10, mem: 12} | |
| freebayes: {cores: 10, mem: 100} | |
| gatk2_base_recalibrator: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx8G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 24 | |
| name: _special | |
| gatk2_depth_of_coverage: {cores: 10, mem: 24} | |
| gatk2_haplotype_caller: {cores: 10, mem: 24} | |
| gatk2_indel_realigner: {mem: 10} | |
| gatk2_print_reads: {cores: 10, mem: 24} | |
| gatk2_realigner_target_creator: {cores: 10, mem: 24} | |
| gatk2_reduce_reads: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx8G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 24 | |
| name: _special | |
| gatk2_unified_genotyper: {cores: 10, mem: 24} | |
| gatk2_variant_annotator: {cores: 10, mem: 24} | |
| gatk2_variant_apply_recalibration: {cores: 10, mem: 24} | |
| gatk2_variant_combine: {cores: 10, mem: 24} | |
| gatk2_variant_eval: {cores: 10, mem: 24} | |
| gatk2_variant_filtration: {mem: 10} | |
| gatk2_variant_recalibrator: {cores: 10, mem: 24} | |
| gatk2_variant_select: {cores: 10, mem: 24} | |
| gatk2_variant_validate: {cores: 10, mem: 24} | |
| gatk_picard_index_builder: {mem: 12} | |
| gemini_load: {cores: 10, mem: 40} | |
| # Permissions | |
| #gemini_query: | |
| # permissions: | |
| # allow: | |
| # roles: | |
| # - admin | |
| ggplot2_heatmap2: {mem: 24} | |
| glassgo: {mem: 4, runner: condor_docker} | |
| graphprot_predict_profile: {mem: 16} | |
| # this tool was developed by IGC Bioinformatics Unit and Daniel Sobral from ELIXIR-PT | |
| # goenrichment: {runner: remote_cluster_mq_pt01} | |
| hammock_1.0: | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 20 | |
| name: java_temp | |
| heatmapper: {mem: 25} | |
| heatmapper_deepTools: {mem: 25} | |
| hicexplorer_hicbuildmatrix: {cores: 10, mem: 160} | |
| hicexplorer_hiccorrectmatrix: {mem: 64} | |
| hicexplorer_hiccorrelate: {mem: 20} | |
| hicexplorer_hicfindtads: {mem: 20} | |
| hicexplorer_hicplotmatrix: {mem: 64} | |
| hicexplorer_hicplottads: {mem: 64} | |
| hicexplorer_hicsummatrices: {mem: 64} | |
| hicexplorer_hicpca: {cores: 10, mem: 60} | |
| hicexplorer_hicmergematrixbins: {mem: 80} | |
| hicexplorer_hictransform: {cores: 10, mem: 60} | |
| hicexplorer_hicplotviewpoint: {mem: 12} | |
| hicexplorer_hicaggregatecontacts: {mem: 12} | |
| hicexplorer_chicaggregatestatistic: {cores: 20, mem: 60} | |
| hicexplorer_chicdifferentialtest: {cores: 20, mem: 60} | |
| hicexplorer_chicplotviewpoint: {cores: 20, mem: 60} | |
| hicexplorer_chicqualitycontrol: {cores: 20, mem: 60} | |
| hicexplorer_chicsignificantinteractions: {cores: 20, mem: 60} | |
| hicexplorer_chicviewpoint: {cores: 20, mem: 60} | |
| hicexplorer_chicviewpointbackgroundmodel: {cores: 20, mem: 60} | |
| schicexplorer_schicdemultiplex: {cores: 5, mem: 64} | |
| schicexplorer_schicadjustmatrix: {cores: 5, mem: 64} | |
| schicexplorer_schiccluster: {cores: 20, mem: 64} | |
| schicexplorer_schiccorrectmatrices: {cores: 20, mem: 110} | |
| schicexplorer_schiccreatebulkmatrix: {cores: 10, mem: 64} | |
| schicexplorer_schicclustercomparments: {cores: 20, mem: 64} | |
| schicexplorer_schicclusterminhash: {cores: 20, mem: 240} | |
| schicexplorer_schicclustersvl: {cores: 20, mem: 20} | |
| schicexplorer_schicconsensusmatrices: {cores: 20, mem: 64} | |
| schicexplorer_schicinfo: {cores: 1, mem: 8} | |
| schicexplorer_schicmergematrixbins: {cores: 20, mem: 64} | |
| schicexplorer_schicmergetoscool: {cores: 20, mem: 64} | |
| schicexplorer_schicnormalize: {cores: 20, mem: 64} | |
| schicexplorer_schicplotclusterprofiles: {cores: 20, mem: 64} | |
| schicexplorer_schicplotconsensusmatrices: {cores: 10, mem: 32} | |
| schicexplorer_schicqualitycontrol: {cores: 20, mem: 64} | |
| hicup_mapper: {cores: 6, mem: 24} | |
| hifiasm: {cores: 32, mem: 48} | |
| hisat: {cores: 10, mem: 20} | |
| # It seems that we are running out of temp space according to error reports from 21.03.2021 | |
| # [E::hts_open_format] Failed to open file "/var/lib/condor/execute/dir_2954912.0000.bam" : No such file or directory | |
| # FATAL: Unable to handle docker://quay.io/biocontainers/mulled-v2-b570fc8a7b25c6a733660cda7e105007b53ac501:26fa90e5bca490ccf5ba8db752fa36fd5834ef00-0 uri: while building SIF from layers: packer failed to pack: while unpacking tmpfs: error unpacking rootfs: unpack layer: unpack entry: usr/local/bin/hisat2-build-l: unpack to regular file: short write: write /var/lib/condor/execute/dir_2147833/build-temp-943357231/rootfs/usr/local/bin/hisat2-build-l: no space left on device | |
| #hisat2: {cores: 8, mem: 20} | |
| hisat2: {cores: 8, mem : 20} | |
| hisat2_index_builder_data_manager: {cores: 10, mem: 180} | |
| hmmer_hmmsearch: {mem: 10} | |
| htseq_count: {mem: 32} | |
| humann2: {cores: 6, mem: 90} | |
| hyphy_busted: {cores: 20, mem: 10} | |
| hyphy_bgm: {cores: 20, mem: 10} | |
| hyphy_gard: {cores: 20, mem: 10} | |
| hyphy_absrel: {cores: 20, mem: 10} | |
| hyphy_fubar: {cores: 20, mem: 10} | |
| hyphy_relax: {cores: 20, mem: 10} | |
| hyphy_fade: {cores: 20, mem: 10} | |
| hyphy_sm19: {cores: 20, mem: 10} | |
| hyphy_meme: {cores: 20, mem: 10} | |
| hyphy_slac: {cores: 20, mem: 10} | |
| hyphy_fel: {cores: 20, mem: 10} | |
| hyphy_prime: {cores: 20} | |
| infernal_cmbuild: {cores: 10, mem: 20} | |
| infernal_cmsearch: {cores: 10, mem: 20} | |
| interproscan: | |
| env: | |
| PATH: $PATH:/data/0/interproscan/interproscan-5.36-75.0/ | |
| mem: 40 | |
| cores: 6 | |
| iqtree: {cores: 10} | |
| iterative_map_pipeline: {mem: 60} | |
| je_clip: {cores: 8} | |
| je_demultiplex: {cores: 8, mem: 20} | |
| je_demultiplex_illu: {cores: 8} | |
| je_markdupes: {cores: 8} | |
| join1: {mem: 18} | |
| #jq: {runner: condor_singularity_with_conda} | |
| kallisto_quant: {cores: 8, mem: 20} | |
| ## uha, with the reference.fa file from the history it is not working? | |
| ## kallisto_quant: {cores: 8, mem: 20_singularity} | |
| lastz_wrapper_2: {mem: 8} | |
| limma_voom: {mem: 4} | |
| lofreq_call: {cores: 2, mem: 8} | |
| khmer_abundance_distribution_single: {cores: 8, mem: 8} | |
| macs2_bdgdiff: {mem: 10} | |
| macs2_callpeak: {mem: 15} | |
| maldi_quant_preprocessing: {mem: 400} | |
| maldi_quant_peak_detection: {mem: 180} | |
| mass_spectrometry_imaging_classification: {mem: 100} | |
| megablast_wrapper: {mem: 20} | |
| meme_dreme: {mem: 16} | |
| meme_fimo: {mem: 4} | |
| merge_pcr_duplicates.py: {mem: 4} | |
| methtools_calling: {cores: 10, mem: 40} | |
| methtools_filter: {mem: 10} | |
| methtools_plot: {cores: 10, mem: 20} | |
| metilene: {cores: 10, mem: 20} | |
| mimodd_varcall: {cores: 6} | |
| minced: {mem: 10} | |
| migmap: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=6G -Xmx90G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 96 | |
| name: java_temp | |
| proteomics_moff: {mem: 20, cores: 6} | |
| metagene_annotator: {mem: 16} | |
| morpheus: | |
| env: | |
| MONO_GC_PARAMS: max-heap-size=2g | |
| mem: 64 | |
| msaboot: {mem: 6} | |
| naive_variant_caller: {mem: 20} | |
| ncbi_blastp_wrapper: {cores: 10, mem: 40, runner: condor_intensive_jobs, force_destination_id: True} | |
| ncbi_blastn_wrapper: {cores: 10, mem: 40} | |
| ncbi_tblastn_wrapper: {cores: 10, mem: 40} | |
| ncbi_blastx_wrapper: {cores: 10, mem: 40} | |
| ncbi_makeblastdb: {mem: 20} | |
| nspdk_sparse: {mem: 16} | |
| numeric_clustering: {mem: 12} | |
| peakachu: {mem: 16} | |
| peptide_shaker: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=4G -Xmx120G -Xms4G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 100 | |
| name: _special | |
| picard_ARRG: {mem: 12} | |
| picard_AddOrReplaceReadGroups: {mem: 12} | |
| picard_BamIndexStats: {mem: 12} | |
| picard_CASM: {mem: 12} | |
| picard_CollectInsertSizeMetrics: {mem: 12} | |
| picard_CollectRnaSeqMetrics: {mem: 12} | |
| picard_DownsampleSam: {mem: 12} | |
| picard_EstimateLibraryComplexity: {mem: 12} | |
| picard_NormalizeFasta: {mem: 12} | |
| picard_FilterSamReads: | |
| env: | |
| TMP_DIR: $TMPDIR | |
| mem: 12 | |
| tmp: large | |
| picard_FixMateInformation: {mem: 12} | |
| picard_FastqToSam: {mem: 12} | |
| picard_MarkDuplicates: | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 12 | |
| name: java_temp | |
| picard_MergeSamFiles: {mem: 12} | |
| picard_QualityScoreDistribution: {mem: 12} | |
| picard_ReorderSam: {mem: 12} | |
| picard_ReplaceSamHeader: {mem: 12} | |
| picard_SamToFastq: {mem: 12} | |
| picard_SortSam: | |
| env: | |
| _JAVA_OPTIONS: -Xmx4G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 10 | |
| name: java_temp | |
| picard_index_builder_data_manager: {mem: 12} | |
| pileometh: {cores: 12, mem: 24} | |
| piranha: {mem: 15} | |
| plotly_regression_performance_plots: {mem: 8} | |
| porechop: {mem: 12} | |
| preproc: {mem: 10} | |
| prokaryotic_ncbi_submission: {cores: 24, mem: 24} | |
| prokka: | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 20 | |
| cores: 8 | |
| proteomics_search_msgfplus_1: {mem: 10} | |
| pyprophet_score: {mem: 400, cores: 1} | |
| pureclip: {mem: 32, cores: 2} | |
| qualimap_bamqc: {mem: 24} | |
| quality_metrics: {mem: 12} | |
| r_correlation_matrix: {mem: 80} | |
| rbc_mirdeep2_mapper: {cores: 10, mem: 20} | |
| rcas: {cores: 4, mem: 16} | |
| ribotaper_ribosome_profiling: {cores: 12, mem: 16} | |
| reactome_pathwaymatcher: | |
| mem: 20 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx17G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| rgEstLibComp: {mem: 12} | |
| rgPicFixMate: {mem: 12} | |
| rgPicardMarkDups: | |
| mem: 12 | |
| env: | |
| _JAVA_OPTIONS: -Xmx12G -Xms1G | |
| rm_spurious_events.py: {mem: 4} | |
| rna_star: {cores: 10, mem: 100} | |
| rna_starsolo: {cores: 4, mem: 40} | |
| rna_star_index_builder_data_manager: | |
| cores: 10 | |
| mem: 300 | |
| params: | |
| local_slots: 6 | |
| rnbeads: {mem: 20} | |
| rsem_calculate_expression: {mem: 16} | |
| rseqc_bam2wig: {cores: 8, mem: 16} | |
| sailfish: {cores: 6, mem: 70} | |
| salmon: {cores: 6, mem: 70} | |
| scanpy_cluster_reduce_dimension: | |
| cores: 4 | |
| 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 | |
| scanpy_filter: | |
| cores: 4 | |
| 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 | |
| scanpy_inspect: | |
| cores: 4 | |
| 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 | |
| scanpy_normalize: | |
| cores: 4 | |
| 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 | |
| scanpy_remove_confounders: | |
| cores: 4 | |
| 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 | |
| scanpy_plot: | |
| cores: 4 | |
| 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 | |
| sam_merge2: | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp | |
| mem: 32 | |
| # samtools_stats: {runner: remote_cluster_mq_de01} | |
| samtools_sort: {cores: 10, mem: 10} | |
| search_gui: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp | |
| mem: 12 | |
| name: special | |
| secretbt2test: {cores: 10, mem: 20} | |
| segemehl: {mem: 80} | |
| seq_filter_by_mapping: {mem: 8} | |
| SiriusAdapter: | |
| mem: 16 | |
| env: | |
| _JAVA_OPTIONS: -Xmx16G -Xms1G | |
| shovill: | |
| cores: 4 | |
| mem: 50 | |
| env: | |
| SHOVILL_RAM: 50 | |
| signalp3: {mem: 10} | |
| smooth_running_window: {mem: 32} | |
| snippy: {mem: 12} | |
| snpEff: {mem: 12} | |
| snpEff_databases: {mem: 12} | |
| snpEff_download: {mem: 12} | |
| snpEff_get_chr_names: {mem: 12} | |
| snpEff_build_gb: | |
| mem: 48 | |
| env: | |
| _JAVA_OPTIONS: -Xmx48G -Xms1G | |
| snpSift_annotate: {mem: 12} | |
| snpSift_caseControl: {mem: 12} | |
| snpSift_filter: {mem: 18} | |
| snpSift_geneSets: {mem: 12} | |
| snpSift_int: {mem: 12} | |
| spades: {cores: 20, mem: 400} | |
| spyboat: {cores: 8, mem: 4} | |
| sshmm: {mem: 16} | |
| structurefold: {mem: 12} | |
| rnaspades: {cores: 10, mem: 300} | |
| stringtie: {mem: 25} | |
| t_coffee: | |
| mem: 100 | |
| env: | |
| DIR_4_TCOFFEE: $TMP | |
| TMP_4_TCOFFEE: $TMP | |
| CACHE_4_TCOFFEE: $TMP | |
| tophat2: {cores: 10, mem: 90} | |
| tp_easyjoin_tool: {mem: 12} | |
| tp_multijoin_tool: {mem: 8} | |
| tp_uniq_tool: {mem: 12} | |
| trimmomatic: | |
| cores: 6 | |
| mem: 12 | |
| name: special | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp | |
| trinity: | |
| cores: 4 | |
| mem: 512 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx170G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp | |
| name: special | |
| umi_tools_group: {mem: 12} | |
| umi_tools_dedup: {mem: 100} | |
| umi_tools_extract: {mem: 4} | |
| unicycler: | |
| cores: 10 | |
| env: | |
| _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp | |
| TERM: vt100 | |
| mem: 100 | |
| name: special | |
| valet: {cores: 8, mem: 20} | |
| varscan_somatic: {cores: 8, mem: 12} | |
| varscan_mpileup: {mem: 12} | |
| varscan_copynumber: {mem: 12} | |
| velvetg: | |
| cores: 4 | |
| env: | |
| OMP_NUM_THREADS: 4 | |
| OMP_THREAD_LIMIT: 4 | |
| mem: 32 | |
| name: _velvetg | |
| velveth: | |
| cores: 4 | |
| env: | |
| OMP_NUM_THREADS: 4 | |
| OMP_THREAD_LIMIT: 4 | |
| mem: 16 | |
| name: _velveth | |
| vsearch_search: {mem: 80} | |
| # Some admin tools | |
| echo_main_env: | |
| permissions: | |
| allow: | |
| roles: | |
| - admin | |
| #tp_awk_tool: | |
| # runner: condor_docker | |
| # permissions: | |
| # allow: | |
| # roles: | |
| # - admin | |
| #tp_replace_in_column: | |
| # permissions: | |
| # allow: | |
| # roles: | |
| # - admin | |
| # permissions testing. | |
| _test_permissions_0: {} | |
| _test_permissions_1: | |
| permissions: | |
| allow: | |
| users: | |
| - b@example.com | |
| _test_permissions_2: | |
| permissions: | |
| allow: | |
| users: | |
| - a@example.com | |
| roles: | |
| - role-b |