Sure! Here's the converted Docker Compose YAML file with a MySQL server as a separate container and a Docker volume for storage:
version: '3'
services:
wandb-local:
image: wandb/local
container_name: wandb-local
environment:
- HOST=https://YOUR_DNS_NAME
| You are an HR specialist and are evaluating the qualifications of job applicants | |
| for a high-performance computing (HPC) specialist position. | |
| You have been given a set of criteria to evaluate each candidate. | |
| The candidate materials are in the attached PDF. | |
| For each job applicant, fill in the following YAML-format criteria document. You | |
| may use the "comment" field to provide additional context or justification for | |
| your evaluation. | |
| --- | |
| # candidate name |
| # convert all CMGD SummarizedExperiments to CSV files | |
| # Should run more-or-less directly as a script | |
| # Requires more than 128GB RAM to complete | |
| # Generates about 200GB of files | |
| # BiocManager::install('curatedMetagenomicData') | |
| # BiocManager::install(c('arrow','data.table','dplyr', 'readr')) | |
| library(curatedMetagenomicData)convert all CMGD SummarizedExperiments to CSV files |
| #!/bin/bash | |
| # results in json format | |
| # Actual data in "results" array | |
| # | |
| # Opportunity numbers taken from https://commonfund.nih.gov/dataecosystem/FundedResearch | |
| curl \ | |
| -X POST \ | |
| https://api.reporter.nih.gov/v2/projects/search \ | |
| -d '{"criteria":{"opportunity_numbers": ["RFA-RM-23-003", "PA20-185", "OTA-23-004", "RFA-RM-22-007", "OTA-23-005", "RFA-RM-17-026", "RFA-RM-21-007", "RFA-RM-19-012"]}}' \ | |
| -H 'Content-Type: application/json' |
| MAIN INFORMATION ABOUT DATA | |
| Timespan 2004 : 2023 | |
| Sources (Journals, Books, etc) 100 | |
| Documents 586 | |
| Annual Growth Rate % 11.38 | |
| Document Average Age 6.51 | |
| Average citations per doc 626.4 | |
| Average citations per year per doc 56.14 | |
| References 10872 |
| { | |
| "accession": "GSE000123", | |
| "files": [ | |
| { | |
| "filetype": "Series SOFT file", | |
| "name": "GSE227465_family.soft.gz", | |
| "size": 23413, | |
| "md5sum": "....", | |
| "created_at": "DATE", | |
| "updated_at": "DATE" |
| --- | |
| format: | |
| html: | |
| mermaid-format: svg | |
| --- | |
| ```{mermaid} | |
| %%| fig-width: 100% | |
| autonumber | |
| Participant C as Client[<font size=6>] |
The ENA browser API https://www.ebi.ac.uk/ena/portal/api/swagger-ui/
There is only limit, no offset. API is designed to simply stream large resultsets
Output as TSV
SEARCH_QUERY='secondary_study_accession=SRP082656' && curl "https://www.ebi.ac.uk/ena/portal/api/search?query=${SEARCH_QUERY}&result=read_run&fields=experiment_accession%2Cexperiment_title%2Csecondary_study_accession%2Caligned%2Caltitude%2Cassembly_quality%2Cassembly_software%2Cbam_aspera%2Cbam_bytes%2Cbam_ftp%2Cbam_galaxy%2Cbam_md5%2Cbase_count%2Cbinning_software%2Cbio_material%2Cbisulfite_protocol%2Cbroad_scale_environmental_context%2Cbroker_name%2Ccage_protocol%2Ccell_line%2Ccell_type%2Ccenter_name%2Cchecklist%2Cchip_ab_provider%2Cchip_protocol%2Cchip_target%2Ccollected_by%2Ccollection_date%2Ccollection_date_end%2Ccollection_date_start%2Ccompleteness_score%2Ccontamination_score%2Ccontrol_experiment%2Ccountry%2Ccultivar%2Cculture_collection%2Cdatahub%2Cdepth%2Cdescription%2Cdev_stage%2Cdnase_protocol%2Cecotype%2
| datasets: | |
| - name: brfss | |
| title: The brfss dataset | |
| description: | | |
| a very long description which can be | |
| in [markdown](https://markdown.org). | |
| - list item | |
| - list item 2 | |
| processor: readr::read_csv | |
| - name: svi |