Migrate a few more entries from EU #103
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@@ -153,7 +153,7 @@ tools: | |
| mem: 30.7 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/.*: | ||
| cores: 20 | ||
| mem: min(max(input_size * 1.2, 3.8), 256) | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/get_online_data/ctb_online_data_fetch/.*: | ||
| mem: 7 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/get_pubchem/ctb_pubchem_download_as_smiles/.*: | ||
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@@ -244,6 +244,9 @@ tools: | |
| mem: 7 | ||
| env: | ||
| CUDA_VISIBLE_DEVICES: 0 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/lirasearch/lirasearch/.*: | ||
| cores: 24 | ||
| mem: 24 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/minced/minced/.*: | ||
| mem: 2 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/.*: | ||
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@@ -273,6 +276,9 @@ tools: | |
| mem: 128 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/numeric_clustering/numeric_clustering/.*: | ||
| mem: 12 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/omark/omark/.*: | ||
| cores: 8 | ||
| mem: 4 | ||
| toolshed.g2.bx.psu.edu/repos/bgruening/openduck_run_smd/openduck_run_smd/.*: | ||
| gpus: 1 | ||
| cores: 1 | ||
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@@ -396,6 +402,9 @@ tools: | |
| mem: 2 | ||
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_sample_filter/dimspy_sample_filter/.*: | ||
| mem: 1 | ||
| toolshed.g2.bx.psu.edu/repos/computational-metabolomics/sirius_csifingerid/sirius_csifingerid/.*: | ||
| cores: 8 | ||
| mem: 8 | ||
| toolshed.g2.bx.psu.edu/repos/computationaltranscriptomics/glassgo/glassgo/.*: | ||
| mem: 1 | ||
| scheduling: | ||
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@@ -574,6 +583,9 @@ tools: | |
| TMP_4_TCOFFEE: $TMP | ||
| toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/.*: | ||
| mem: 16 | ||
| toolshed.g2.bx.psu.edu/repos/ecology/wildlife_megadetector_huggingface/wildlife_megadetector_huggingface/.*: | ||
| gpus: 1 | ||
| mem: 20 | ||
| toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/.*: | ||
| mem: 1 | ||
| toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/biosigner/.*: | ||
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@@ -644,7 +656,9 @@ tools: | |
| mem: 16 | ||
| toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/.*: | ||
| cores: 8 | ||
| mem: 24 | ||
| env: | ||
| EGGNOG_DBMEM: --dbmem | ||
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Member
Author
There was a problem hiding this comment. I have a related question here. @cat-bro do you know if on AU all those envs are passed into the containers without any extra magic? |
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| toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper_search/.*: | ||
| cores: 4 | ||
| mem: 20 | ||
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@@ -1095,6 +1109,18 @@ tools: | |
| toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*: | ||
| cores: 16 | ||
| mem: 61.4 | ||
| toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/.*: | ||
| cores: 4 | ||
| mem: 30 | ||
| scheduling: | ||
| require: | ||
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Member
Author
There was a problem hiding this comment. I can remove that. But what is the preferred way to indicate that this tool can/should run in Singularity? |
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| - singularity | ||
| rules: | ||
| - id: tpvdb_helixer_large_gpu_rule | ||
| if: input_size >= 0.01 | ||
| gpus: 1 | ||
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Member
Author
There was a problem hiding this comment. flag GPU here, if we don't want this in a shared DB. |
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| params: | ||
| singularity_run_extra_arguments: ' --nv ' | ||
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Member
Author
There was a problem hiding this comment. this is enabling Singularity containers to setup the containers for GPU/Nvidia ...
Collaborator
There was a problem hiding this comment. My initial thought would be: keep this but remove the scheduling tag for singularity and add a comment? But in general running things in singularity is the recommended approach, or not? |
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| toolshed.g2.bx.psu.edu/repos/goeckslab/image_learner/image_learner/.*: | ||
| cores: 8 | ||
| mem: 32 | ||
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@@ -1147,8 +1173,14 @@ tools: | |
| toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/.*: | ||
| mem: 15.2 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/.*: | ||
| cores: 1 | ||
| mem: 16 | ||
| rules: | ||
| - id: tpvdb_anndata_manipulate_rule | ||
| if: | | ||
| param_dict = job.get_param_values(app) | ||
| param_dict.get('manipulate', {}).get('function') == 'concatenate' | ||
| mem: 60 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/.*: | ||
| mem: 8 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/arriba/arriba/.*: | ||
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@@ -1339,8 +1371,14 @@ tools: | |
| toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1: | ||
| cores: 3 | ||
| mem: 3.7 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/.*: | ||
| cores: 3 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*: | ||
| mem: 11.4 | ||
| rules: | ||
| - id: tpvdb_fasta_stats_large_rule | ||
| if: input_size >= 0.01 | ||
| cores: 3 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/.*: | ||
| cores: 4 | ||
| mem: min(max(int(input_size * 6), 8), 58) | ||
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@@ -1547,7 +1585,7 @@ tools: | |
| cores: 8 | ||
| mem: 8 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/.*: | ||
| cores: 16 | ||
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Member
Author
There was a problem hiding this comment. We have way more cores on EU ... but the memory rule here is very sophisticated ... maybe both? |
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| mem: | | ||
| import os | ||
| import functools | ||
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@@ -2338,6 +2376,13 @@ tools: | |
| toolshed.g2.bx.psu.edu/repos/iuc/nanopolishcomp_eventaligncollapse/nanopolishcomp_eventaligncollapse/.*: | ||
| cores: 10 | ||
| mem: 12 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/.*: | ||
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Member
Author
There was a problem hiding this comment. This is a very expensive and inefficient tool for VGP - TODO look at ORGs rule. |
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| rules: | ||
| - id: tpvdb_ncbi_fcs_gx_screen_mode_rule | ||
| if: | | ||
| helpers.job_args_match(job, app, {"mode": {"mode_selector": "screen"}}) | ||
| cores: 64 | ||
| mem: 480 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/novoplasty/novoplasty/.*: | ||
| mem: 40 | ||
| rules: | ||
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@@ -2413,8 +2458,10 @@ tools: | |
| toolshed.g2.bx.psu.edu/repos/iuc/pureclip/pureclip/.*: | ||
| cores: 2 | ||
| mem: 32 | ||
| # 4GB is enough for most of the runs as it seems | ||
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Member
Author
There was a problem hiding this comment. I had this in my notes, no idea why we have here so much more memory :( |
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| toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/.*: | ||
| cores: 1 | ||
| mem: 6 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/.*: | ||
| cores: 6 | ||
| mem: 24 | ||
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@@ -2637,10 +2684,23 @@ tools: | |
| toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/.*: | ||
| mem: 8 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/.*: | ||
| cores: 24 | ||
| mem: 250 | ||
| env: | ||
| _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G | ||
| rules: | ||
| - id: tpvdb_trinity_small_rule | ||
| if: input_size < 0.1 | ||
| cores: 1 | ||
| mem: 4 | ||
| - id: tpvdb_trinity_medium_rule | ||
| if: 0.1 <= input_size < 1 | ||
| cores: 12 | ||
| mem: 92 | ||
| - id: tpvdb_trinity_fail_rule | ||
| if: input_size >= 1 | ||
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Member
Author
There was a problem hiding this comment. We are bailing out when we see large files and recommend Spades. |
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| fail: | | ||
| Too much data, we cannot support such large Trinity assemblies. Please use RNAspades instead. | ||
| toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/.*: | ||
| mem: 8 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/.*: | ||
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@@ -2680,6 +2740,15 @@ tools: | |
| scheduling: | ||
| accept: | ||
| - pulsar | ||
| rules: | ||
| - id: tpvdb_unicycler_small_input_rule | ||
| if: input_size < 0.05 | ||
| cores: 1 | ||
| mem: 3.8 | ||
| - id: tpvdb_unicycler_medium_input_rule | ||
| if: 0.05 <= input_size < 2 | ||
| cores: 8 | ||
| mem: 28 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/valet/valet/.*: | ||
| cores: 8 | ||
| mem: 20 | ||
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@@ -2701,6 +2770,9 @@ tools: | |
| toolshed.g2.bx.psu.edu/repos/iuc/vcf2maf/vcf2maf/.*: | ||
| cores: 6 | ||
| mem: 23.0 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/.*: | ||
| cores: 4 | ||
| mem: 100 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/vsearch/.*: | ||
| mem: 8 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_alignment/.*: | ||
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Is it ok to specify here GPUs?
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If it doesn't work without I would say yes