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) removes (guix hash) and (guix pk-crypto), which now live as part of Guile-Gcrypt (version 0.1.0.) * guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm, tests/hash.scm, tests/pk-crypto.scm: Remove. * configure.ac: Test for Guile-Gcrypt. Remove LIBGCRYPT and LIBGCRYPT_LIBDIR assignments. * m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove. * README: Add Guile-Gcrypt to the dependencies; move libgcrypt as "required unless --disable-daemon". * doc/guix.texi (Requirements): Likewise. * gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm, guix/git.scm, guix/http-client.scm, guix/import/cpan.scm, guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm, guix/import/gnu.scm, guix/import/hackage.scm, guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm, guix/pki.scm, guix/scripts/archive.scm, guix/scripts/authenticate.scm, guix/scripts/download.scm, guix/scripts/hash.scm, guix/scripts/pack.scm, guix/scripts/publish.scm, guix/scripts/refresh.scm, guix/scripts/substitute.scm, guix/store.scm, guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm, tests/builders.scm, tests/challenge.scm, tests/cpan.scm, tests/crate.scm, tests/derivations.scm, tests/gem.scm, tests/nar.scm, tests/opam.scm, tests/pki.scm, tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm, tests/store.scm, tests/substitute.scm: Adjust imports. * gnu/system/vm.scm: Likewise. (guile-sqlite3&co): Rename to... (gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT. (expression->derivation-in-linux-vm)[config]: Remove. (iso9660-image)[config]: Remove. (qemu-image)[config]: Remove. (system-docker-image)[config]: Remove. * guix/scripts/pack.scm: Adjust imports. (guile-sqlite3&co): Rename to... (gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT. (self-contained-tarball)[build]: Call 'make-config.scm' without #:libgcrypt argument. (squashfs-image)[libgcrypt]: Remove. [build]: Call 'make-config.scm' without #:libgcrypt. (docker-image)[config, json]: Remove. [build]: Add GUILE-GCRYPT to the extensions Remove (guix config) from the imported modules. * guix/self.scm (specification->package): Remove "libgcrypt", add "guile-gcrypt". (compiled-guix): Remove #:libgcrypt. [guile-gcrypt]: New variable. [dependencies]: Add it. [*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call. Add #:extensions. [*config*]: Remove #:libgcrypt from 'make-config.scm' call. (%dependency-variables): Remove %libgcrypt. (make-config.scm): Remove #:libgcrypt. * build-aux/build-self.scm (guile-gcrypt): New variable. (make-config.scm): Remove #:libgcrypt. (build-program)[fake-gcrypt-hash]: New variable. Add (gcrypt hash) to the imported modules. Adjust load path assignments. * gnu/packages/package-management.scm (guix)[propagated-inputs]: Add GUILE-GCRYPT. [arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search path.