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' |
| library(GenomicDataCommons) | |
| library(magrittr) | |
| TCGAtranslateID = function(file_ids) { | |
| info = files() %>% | |
| GenomicDataCommons::filter( ~ file_id %in% file_ids) %>% | |
| GenomicDataCommons::select('cases.samples.submitter_id') %>% | |
| results_all() | |
| # The mess of code below is to extract TCGA barcodes | |
| # id_list will contain a list (one item for each file_id) |
| 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 |
| "title" "gpl" "bioc_package" "manufacturer" "organism" "data_row_count" | |
| "Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I" "GPL15380" "GGHumanMethCancerPanelv1" "Illumina" "Homo sapiens" 1536 | |
| "Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)" "GPL8490" "IlluminaHumanMethylation27k" "Illumina, Inc." "Homo sapiens" 27578 | |
| "Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)" "GPL13534" "IlluminaHumanMethylation450k" "Illumina, Inc." "Homo sapiens" 485577 | |
| "GE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray" "GPL2898" "adme16cod" "GE Healthcare" "Rattus norvegicus" 1280 | |
| "[AG] Affymetrix Arabidopsis Genome Array" "GPL71" "ag" "Affymetrix" "Arabidopsis thaliana" 8297 | |
| "[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array" "GPL198" "ath1121501" "Affymetrix" "Arabidopsis thaliana" 22810 | |
| "[Bovine] Affymetrix Bovine Genome Array" "GPL2112" "bovine" "Affymetrix" "Bos taurus" 24128 | |
| "[Canine] Affymetrix Canine Genome 1.0 Array" "GPL39 |
| { | |
| "accession": "GSE000123", | |
| "files": [ | |
| { | |
| "filetype": "Series SOFT file", | |
| "name": "GSE227465_family.soft.gz", | |
| "size": 23413, | |
| "md5sum": "....", | |
| "created_at": "DATE", | |
| "updated_at": "DATE" |