Genome#

Get all organism available on remote server that have genome data available:#

• URL: /genomics/taxonomies/
• Method: GET
• Parameters: NONE
• Example:

curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxx" \
 https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/

Get all genome types (remote databases) that support given organism. Right now there is only one available: UCSC#

• URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/
• Method: GET
• Parameters:
  • taxonomyId - organism taxonomy
• Example:

curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxx" \
 https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/

Get all available genome versions for specified organism and genome type:#

• URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions
• Method: GET
• Parameters:
  • taxonomyId - organism taxonomy
  • genomeType - remote database where we want to check versions (for now, only UCSC is supported)
• Example:

curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxx" \
 https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/UCSC/versions

Get remote url for specified genome, version, and remote database:#

• URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions/{version}:getAvailableRemoteUrls
• Method: GET
• Parameters:
  • taxonomyId - organism taxonomy
  • genomeType - remote database where we want to check versions (for now, only UCSC is supported)
  • version - version of the genome that we are interested in
• Example:

curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxx" \
 https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38:getAvailableRemoteUrls

Start downloading genome data from remote database to minerva:#

• URL: /genomics/
• Method: POST
• Parameters:
  • organismId - organism taxonomy
  • type - remote database where we want to check versions (for now, only UCSC is supported)
  • version - version of the genome that we are interested in
  • sourceUrl - url to 2bit file with genome
• Example:

curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
 --data "organismId=9606&type=UCSC&version=hg38&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg38%2FbigZips%2Fhg38.2bit"
 https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/

Get information about specific downloaded genome:#

• URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions/{version}/
• Method: GET
• Parameters:
  • organismId - organism taxonomy
  • type - remote database where we want to check versions (for now, only UCSC is supported)
  • version - version of the genome that we are interested in
• Example:

curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/

Get information about all downloaded genomes:#

• URL: /genomics/
• Method: GET
• Parameters: NONE
• Example:

curl -X GET --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/

Delete downloaded genome:#

• URL: /genomics/{genomeId}/
• Method: DELETE
• Parameters:
  • genomeId - id of the downloaded genome
• Example:

curl -X DELETE --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/12345/

Gene mapping#

Add gene mapping:#

• URL: /genomics/{genomeId}/geneMapping/
• Method: POST
• Parameters:
  • genomeId - id of the downloaded genome
  • name - name of the mapping
  • url - url to big bed file with gene mapping
• Example:

curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
--data "name=mappingName&url=https%3A%2F%2Fminerva-dev.lcsb.uni.lu%2Ftmp%2FrefGene.bb"
https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/12345/

Delete gene mapping:#

• URL: /genomics/{genomeId}/geneMapping/{geneMappingId}
• Method: DELETE
• Parameters:
  • genomeId - id of the downloaded genome
  • geneMappingId - id of the gene mapping
• Example:

curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/12345/geneMapping/32/