def plot_reads_in_genes_R(input_files, output_files): job_script = 'src/R/plot_reads_in_genes.R' ntasks = '1' cpus_per_task = '1' job_name = 'plot_reads_in_genes' job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name) functions.print_job_submission(job_name, job_id)
def combine_mfuzz_results_R(input_files, output_files): job_script = 'src/R/combine_mfuzz_results.R' ntasks = '1' cpus_per_task = '1' job_name = 'mfuzz_plot' job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name) functions.print_job_submission(job_name, job_id)
def parse_star_stats_R(input_files, output_files): job_script = 'src/R/parse_star_stats.R' ntasks = '1' cpus_per_task = '1' job_name = 'parse_stats' job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name) functions.print_job_submission(job_name, job_id)
def compare_saito_genes_R(input_files, output_files): job_script = 'src/R/compare_saito_genes.R' ntasks = '1' cpus_per_task = '1' job_name = 'saito_genes' job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name) functions.print_job_submission(job_name, job_id)
def deseq2_R(input_files, output_files, species): job_script = 'src/R/deseq2.R' ntasks = '1' cpus_per_task = '1' job_name = species + '_deseq' job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name, extras=['-s', species]) functions.print_job_submission(job_name, job_id)
def star(input_files, output_files, species): job_script = 'src/sh/star' ntasks = '1' cpus_per_task = '7' job_name = species + '_star' job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name, extras=['-s', species]) functions.print_job_submission(job_name, job_id)
def generate_index(input_files, output_files, species): job_script = 'src/sh/generate_index' ntasks = '1' cpus_per_task = '7' job_name = species + "_index" job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name, extras=['-s', species]) functions.print_job_submission(job_name, job_id)
def download_genome(output_files, species, genome_url, annotation_url, jgi_logon, jgi_password): job_script = 'src/sh/download_genomes' ntasks = '1' cpus_per_task = '1' job_name = species + "_dl" jgi_prefix = 'http://genome.jgi.doe.gov' job_id = functions.submit_job(job_script, ntasks, cpus_per_task, job_name, extras=['-e', jgi_logon, '-p', jgi_password, '-s', species, '-g', jgi_prefix + genome_url, '-a', jgi_prefix + annotation_url]) functions.print_job_submission(job_name, job_id)