1 files changed, 0 insertions, 69 deletions
diff --git a/gnu/packages/patches/grocsvs-dont-use-admiral.patch b/gnu/packages/patches/grocsvs-dont-use-admiral.patch
deleted file mode 100644
index cb976e19b0..0000000000
--- a/gnu/packages/patches/grocsvs-dont-use-admiral.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-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)