[PATCH] gnu: Add grocsvs.

DoneSubmitted by Efraim Flashner.
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  • Efraim Flashner
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Efraim Flashner wrote on 21 Apr 12:57 +0200
(address . guix-patches@gnu.org)(name . Efraim Flashner)(address . efraim@flashner.co.il)
20200421105717.28383-1-efraim@flashner.co.il
* 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.--- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 42 +++++++++++ .../patches/grocsvs-dont-use-admiral.patch | 69 +++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 gnu/packages/patches/grocsvs-dont-use-admiral.patch
Toggle diff (146 lines)diff --git a/gnu/local.mk b/gnu/local.mkindex ca863a8b9b..c24ff3c85d 100644--- a/gnu/local.mk+++ b/gnu/local.mk@@ -996,6 +996,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \+ %D%/packages/patches/grocsvs-dont-use-admiral.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex b9be0c1918..dae42df0dc 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -79,6 +79,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph)+ #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile)@@ -15710,3 +15711,44 @@ biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.") (license license:lgpl2.1+)))++(define-public grocsvs+ ;; The last release is out of date and new features have been added.+ (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d")+ (revision "1"))+ (package+ (name "grocsvs")+ (version (git-version "0.2.6.1" revision commit))+ (source (origin+ (method git-fetch)+ (uri (git-reference+ (url "https://github.com/grocsvs/grocsvs")+ (commit commit)))+ (file-name (git-file-name name version))+ (sha256+ (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc"))+ (patches (search-patches "grocsvs-dont-use-admiral.patch"))))+ (build-system python-build-system)+ (arguments+ `(#:tests? #f ; No test suite.+ #:python ,python-2)) ; Only python-2 supported.+ (inputs+ `(("python2-h5py" ,python2-h5py)+ ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper)+ ("python2-networkx" ,python2-networkx)+ ("python2-psutil" ,python2-psutil)+ ("python2-pandas" ,python2-pandas)+ ("python2-pybedtools" ,python2-pybedtools)+ ("python2-pyfaidx" ,python2-pyfaidx)+ ("python2-pygraphviz" ,python2-pygraphviz)+ ("python2-pysam" ,python2-pysam)+ ("python2-scipy" ,python2-scipy)))+ (home-page "https://github.com/grocsvs/grocsvs")+ (synopsis "Genome-wide reconstruction of complex structural variants")+ (description+ "@dfn{Genome-wide Reconstruction of Complex Structural Variants}+(GROC-SVs) is a software pipeline for identifying large-scale structural+variants, performing sequence assembly at the breakpoints, and reconstructing+the complex structural variants using the long-fragment information from the+10x Genomics platform.")+ (license license:expat))))diff --git a/gnu/packages/patches/grocsvs-dont-use-admiral.patch b/gnu/packages/patches/grocsvs-dont-use-admiral.patchnew file mode 100644index 0000000000..cb976e19b0--- /dev/null+++ b/gnu/packages/patches/grocsvs-dont-use-admiral.patch@@ -0,0 +1,69 @@+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)-- 2.26.2
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Efraim Flashner wrote on 5 May 09:35 +0200
Re: bug#40743: Acknowledgement ([PATCH] gnu: Add grocsvs.)
(address . 40743-done@debbugs.gnu.org)
20200505073516.GJ1920@E5400
Patch pushed

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