JoshuaTree2.py
def run_cactus(fasta_output_path,cactus_run_directory,cactus_softlink, n_cpus, hal2maf_softlink, nickname_file, fasta_path, submission_system, shifter): #fixme get rid of '' and add to command line tool
    """Run multiple sequence alignment via Progressive Cactus on multiple species synteny blocks and export as maf files. Try to run softlink_cactus beforehand, else use official cactus paths instead of softlinks."""
    cactus_run_obj = CactusRun(fasta_output_path,cactus_run_directory,cactus_softlink, nickname_file, fasta_path)
    cactus_run_obj.write_fastas_seqfile()
    cactus_run_obj.run_cactus(submission_system, shifter=shifter)
    cactus_run_obj.hal2maf(n_cpus, hal2maf_softlink)
Run multiple sequence alignment via Progressive Cactus on multiple species synteny blocks and export as maf files. Try to run softlink_cactus beforehand, else use official cactus paths instead of softlinks.
Run multiple sequence alignment via Progressive Cactus on multiple species synteny blocks and export as maf files. Try to run softlink_cactus beforehand, else use official cactus paths instead of softlinks.
Run multiple sequence alignment via Progressive Cactus on multiple species synteny blocks and export as maf files . Try to run softlink_cactus beforehand else use official cactus paths instead of softlinks .
def run_cactus(fasta_output_path,cactus_run_directory,cactus_softlink, n_cpus, hal2maf_softlink, nickname_file, fasta_path, submission_system, shifter): 
    cactus_run_obj = CactusRun(fasta_output_path,cactus_run_directory,cactus_softlink, nickname_file, fasta_path)
    cactus_run_obj.write_fastas_seqfile()
    cactus_run_obj.run_cactus(submission_system, shifter=shifter)
    cactus_run_obj.hal2maf(n_cpus, hal2maf_softlink)
def run_cactus ( fasta_output_path , cactus_run_directory , cactus_softlink , n_cpus , hal2maf_softlink , nickname_file , fasta_path , submission_system , shifter ) : cactus_run_obj = CactusRun ( fasta_output_path , cactus_run_directory , cactus_softlink , nickname_file , fasta_path ) cactus_run_obj . write_fastas_seqfile ( ) cactus_run_obj . run_cactus ( submission_system , shifter = shifter ) cactus_run_obj . hal2maf ( n_cpus , hal2maf_softlink )
Run multiple sequence alignment via Progressive Cactus on multiple species synteny blocks and export as maf files.
Run multiple sequence alignment via Progressive Cactus on multiple species synteny blocks and export as maf files .
#fixme get rid of '' and add to command line tool """Run multiple sequence alignment via Progressive Cactus on multiple species synteny blocks and export as maf files. Try to run softlink_cactus beforehand, else use official cactus paths instead of softlinks."""
fasta_output_path
cactus_run_directory
cactus_softlink
n_cpus
hal2maf_softlink
nickname_file
fasta_path
submission_system
shifter