python-admiral doesn't have a license https://github.com/nspies/admiral/issues/3 diff --git a/setup.py b/setup.py index 692b6a0..568f381 100755 --- a/setup.py +++ b/setup.py @@ -20,7 +20,7 @@ setup( 'console_scripts' : ["grocsvs = grocsvs.main:main"] }, - install_requires = ["admiral", "h5py", "networkx>=2.0", "pandas", "pybedtools", + install_requires = ["h5py", "networkx>=2.0", "pandas", "pybedtools", "pyfaidx", "pysam>=0.10.0", "scipy", "ipython-cluster-helper", "pygraphviz", "psutil"], diff --git a/src/grocsvs/jobmanagers.py b/src/grocsvs/jobmanagers.py index 6da0b58..112d7ff 100755 --- a/src/grocsvs/jobmanagers.py +++ b/src/grocsvs/jobmanagers.py @@ -41,34 +41,3 @@ class MultiprocessingCluster(Cluster): pool = multiprocessing.Pool(processes=self.processes) return pool.map_async(fn, args).get(999999) - -class AdmiralCluster(Cluster): - def map(self, fn, args): - from admiral import jobmanagers, remote - - cluster_options = self.cluster_settings.cluster_options.copy() - - scheduler = cluster_options.pop("scheduler") - - jobmanager_class = jobmanagers.get_jobmanager(scheduler) - jobmanager = jobmanager_class( - batch_dir=self.batch_dir, log_dir=self.batch_dir) - - - if not "mem" in cluster_options: - cluster_options["mem"] = "16g" - if not "time" in cluster_options: - cluster_options["time"] = "12h" - - jobs = [] - #for i, arg in enumerate(args): - - job_name = args[0].__class__.__name__ - args = [[arg] for arg in args] - job = remote.run_remote(fn, jobmanager, job_name, args=args, - array=True, overwrite=True, **cluster_options) - - result = jobmanagers.wait_for_jobs([job], wait=5, progress=True) - - if not result: - raise Exception("Some chunks failed to complete") diff --git a/src/grocsvs/pipeline.py b/src/grocsvs/pipeline.py index ab1bb2d..350976f 100755 --- a/src/grocsvs/pipeline.py +++ b/src/grocsvs/pipeline.py @@ -8,8 +8,7 @@ from grocsvs import utilities def make_jobmanager(jobmanager_settings, processes, batch_dir): jobmanager_classes = {"IPCluster":jobmanagers.IPCluster, "local": jobmanagers.LocalCluster, - "multiprocessing": jobmanagers.MultiprocessingCluster, - "admiral": jobmanagers.AdmiralCluster} + "multiprocessing": jobmanagers.MultiprocessingCluster} cls = jobmanager_classes[jobmanager_settings.cluster_type] return cls(processes, jobmanager_settings, batch_dir)