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)
