31def9a9df
* gnu/packages/bioinformatics.scm (grocsvs): New variable. * gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
69 lines
2.7 KiB
Diff
69 lines
2.7 KiB
Diff
python-admiral doesn't have a license
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https://github.com/nspies/admiral/issues/3
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diff --git a/setup.py b/setup.py
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index 692b6a0..568f381 100755
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--- a/setup.py
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+++ b/setup.py
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@@ -20,7 +20,7 @@ setup(
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'console_scripts' : ["grocsvs = grocsvs.main:main"]
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},
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- install_requires = ["admiral", "h5py", "networkx>=2.0", "pandas", "pybedtools",
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+ install_requires = ["h5py", "networkx>=2.0", "pandas", "pybedtools",
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"pyfaidx", "pysam>=0.10.0", "scipy", "ipython-cluster-helper",
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"pygraphviz", "psutil"],
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diff --git a/src/grocsvs/jobmanagers.py b/src/grocsvs/jobmanagers.py
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index 6da0b58..112d7ff 100755
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--- a/src/grocsvs/jobmanagers.py
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+++ b/src/grocsvs/jobmanagers.py
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@@ -41,34 +41,3 @@ class MultiprocessingCluster(Cluster):
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pool = multiprocessing.Pool(processes=self.processes)
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return pool.map_async(fn, args).get(999999)
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-
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-class AdmiralCluster(Cluster):
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- def map(self, fn, args):
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- from admiral import jobmanagers, remote
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-
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- cluster_options = self.cluster_settings.cluster_options.copy()
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-
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- scheduler = cluster_options.pop("scheduler")
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-
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- jobmanager_class = jobmanagers.get_jobmanager(scheduler)
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- jobmanager = jobmanager_class(
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- batch_dir=self.batch_dir, log_dir=self.batch_dir)
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-
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-
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- if not "mem" in cluster_options:
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- cluster_options["mem"] = "16g"
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- if not "time" in cluster_options:
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- cluster_options["time"] = "12h"
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-
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- jobs = []
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- #for i, arg in enumerate(args):
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-
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- job_name = args[0].__class__.__name__
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- args = [[arg] for arg in args]
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- job = remote.run_remote(fn, jobmanager, job_name, args=args,
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- array=True, overwrite=True, **cluster_options)
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-
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- result = jobmanagers.wait_for_jobs([job], wait=5, progress=True)
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-
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- if not result:
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- raise Exception("Some chunks failed to complete")
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diff --git a/src/grocsvs/pipeline.py b/src/grocsvs/pipeline.py
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index ab1bb2d..350976f 100755
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--- a/src/grocsvs/pipeline.py
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+++ b/src/grocsvs/pipeline.py
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@@ -8,8 +8,7 @@ from grocsvs import utilities
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def make_jobmanager(jobmanager_settings, processes, batch_dir):
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jobmanager_classes = {"IPCluster":jobmanagers.IPCluster,
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"local": jobmanagers.LocalCluster,
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- "multiprocessing": jobmanagers.MultiprocessingCluster,
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- "admiral": jobmanagers.AdmiralCluster}
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+ "multiprocessing": jobmanagers.MultiprocessingCluster}
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cls = jobmanager_classes[jobmanager_settings.cluster_type]
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return cls(processes, jobmanager_settings, batch_dir)
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