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) ...* gnu/system.scm (operating-system-directory-base-entries): Return a regular, non-monadic value. * gnu/services.scm (system-derivation): Adjust accordingly. * gnu/system/linux-container.scm (container-essential-services): Likewise. Ludovic Courtès 2020-04-26services: profile: Use a declarative profile....* gnu/services.scm (packages->profile-entry): Use 'profile' instead of 'profile-derivation'. Ludovic Courtès 2020-04-21services: etc: Detect and report duplicate entries....Fixes <https://bugs.gnu.org/40729>. Reported by Christopher Baines <mail@cbaines.net>. * gnu/services.scm (files->etc-directory)[assert-no-duplicates]: New procedure. Use it. Ludovic Courtès 2020-04-05services: Allow modprobe to use "/etc/modprobe.d"....* gnu/services.scm (%modprobe-wrapper): Set 'MODPROBE_OPTIONS' environment variable. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Brice Waegeneire 2020-04-02services: Accumulate builds for 'system' entries....That way, more build requests are accumulated when running "guix system build". * gnu/services.scm (system-derivation): Use 'mapm/accumulate-builds' rather than 'sequence'. Ludovic Courtès 2019-12-07services: Add 'provenance-service-type'....* gnu/services.scm (object->pretty-string) (channel->code, channel->sexp, provenance-file) (provenance-entry): New procedures. (provenance-service-type): New variable. * gnu/system.scm (operating-system-with-provenance): New procedure. * doc/guix.texi (Service Reference): Document 'provenance-service-type'. Ludovic Courtès 2019-11-09services: 'fold-services' memoizes service values....Previously 'fold-services' could end up traversing the same services in the graph several times, which is what this change addresses. The hit rate on the 'add-data-to-store' cache goves from 9% to 8% on "guix system build desktop.tmpl -nd", and the number of lookups in that cache goes from 4458 to 4383. * gnu/services.scm (fold-services): Turn 'loop' into a monadic procedure in %STATE-MONAD and use it to memoize values of visited services. Ludovic Courtès 2019-08-14remote: Remove '--system' argument....* gnu/services.scm (activation-script): Return a <program-file> rather than a <scheme-file>. * gnu/deploy.scm (guix-deploy): Remove handling for '--system'. (show-help): Remove documentation for '--system'. (%default-options): Remove default setting for 'system'. Jakob L. Kreuze 2019-05-10services: 'gc-root-service-type' now has a default value....* gnu/services.scm (gc-root-service-type)[default-value]: New field. Ludovic Courtès 2018-09-07