comparison bdss_client_sra_se.Rmd @ 15:fe5f30584308 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty

14:c0b8476fbc85

    # build URL from SRA accession
    url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
                 substr(id, 1, 3), '/',
                 substr(id, 1, 6), '/', id, '/', id, '.sra')
    # download sra file with bdss
    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
    system(bdss_command, intern = TRUE)
    # convert .sra to .fastq/.fasta
    if('FORMAT' == 'fasta') {
      command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id)
    } else {

    # list all fastq files
    all_fastq_files = strsplit(getURL(url_base, dirlistonly = TRUE), split = '\n')[[1]]
    if (length(all_fastq_files) == 1) {
      # this is a single end SRA file. build url to download fastq
      url = paste0(url_base, '/', all_fastq_files)
      bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
      run_bdss = system(bdss_command, intern = TRUE)
      print(run_bdss)
    } else {
      print(paste0('Two fastq files found for this SRA accession: ', id))
      print('Downloading skipped for ', id)
      # url_1 = paste0(url_base, '/', all_fastq_files[1])
      # bdss_command_1 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_1)
      # run_bdss_1 = system(bdss_command, intern = TRUE)
      # url_2 = paste0(url_base, '/', all_fastq_files[1])
      # bdss_command_2 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_2)
      # run_bdss_2 = system(bdss_command, intern = TRUE)
    }
  }
  
}

15:fe5f30584308

    # build URL from SRA accession
    url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
                 substr(id, 1, 3), '/',
                 substr(id, 1, 6), '/', id, '/', id, '.sra')
    # download sra file with bdss
    bdss_command = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
    system(bdss_command, intern = TRUE)
    # convert .sra to .fastq/.fasta
    if('FORMAT' == 'fasta') {
      command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id)
    } else {

    # list all fastq files
    all_fastq_files = strsplit(getURL(url_base, dirlistonly = TRUE), split = '\n')[[1]]
    if (length(all_fastq_files) == 1) {
      # this is a single end SRA file. build url to download fastq
      url = paste0(url_base, '/', all_fastq_files)
      bdss_command = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
      run_bdss = system(bdss_command, intern = TRUE)
      print(run_bdss)
    } else {
      print(paste0('Two fastq files found for this SRA accession: ', id))
      print('Downloading skipped for ', id)
      # url_1 = paste0(url_base, '/', all_fastq_files[1])
      # bdss_command_1 = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url_1)
      # run_bdss_1 = system(bdss_command, intern = TRUE)
      # url_2 = paste0(url_base, '/', all_fastq_files[1])
      # bdss_command_2 = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url_2)
      # run_bdss_2 = system(bdss_command, intern = TRUE)
    }
  }
  
}