def is_exec(program): """checks if a program is in the global path and executable""" cmd = ['which', program] try: return procOps.call_proc_lines(cmd)[0].endswith(program) except ProcException: return False
def samtools_version(): """checks the version of samtools installed""" try: r = procOps.call_proc_lines(['samtools', '--version']) if StrictVersion(r[0].split()[1].split('-')[0]) < '1.3': raise ToolMissingException('samtools version is not >= 1.3.0') except ProcException: raise ToolMissingException('samtools is not installed')
def samtools_version(): """checks the version of samtools installed""" try: r = procOps.call_proc_lines(['samtools', '--version']) if StrictVersion(r[0].split()[1].split('-')[0]) < '1.3': raise ToolMissingException('samtools version is not >= 1.3.0') except ProcException: raise ToolMissingException('samtools is not installed')
def get_tree(hal): """ Extracts a Tree object from a HAL :param hal: HAL file. :return: Tree object """ cmd = ['halStats', '--tree', hal] newick = call_proc_lines(cmd)[0] return ete3.Tree(newick, format=1)
def get_tree(hal): """ Extracts a Tree object from a HAL :param hal: HAL file. :return: Tree object """ cmd = ['halStats', '--tree', hal] newick = call_proc_lines(cmd)[0] return ete3.Tree(newick, format=1)
def is_exec(program): """checks if a program is in the global path and executable""" if running_in_container(): # We assume containerized versions don't need to check if the # tools are installed--they definitely are, and calling docker # just to run "which" can be surprisingly expensive. But we do # check for the presence of Docker, since that should take # only a few ms. cmd = ['which', 'docker'] pl = Procline(cmd, stdin='/dev/null', stdout='/dev/null', stderr='/dev/null') try: pl.wait() except ProcException: raise ToolMissingException("Docker not found. Either install Docker, or install CAT's dependencies and use --binary-mode local.") cmd = ['which', program] try: return procOps.call_proc_lines(cmd)[0].endswith(program) except ProcException: return False