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path: root/gnu/packages/patches/grocsvs-dont-use-admiral.patch
blob: cb976e19b0f55a4b1ac2d8313e42698ad6e3c41f (about) (plain)
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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)