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)
>| Author |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|