Merge branch 'master' of /home/git/public/guix-bioinformatics

1 files changed, 83 insertions, 1 deletions

diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index a327187..fe5fcb2 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -1,10 +1,19 @@
 (define-module (gn packages cwl)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix packages)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
-  #:use-module (gnu packages bioinformatics))
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages docker)
+  #:use-module (gnu packages node)
+  #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages time)
+  #:use-module (gn packages python))
 
 
 (define-public cwl-runner
@@ -28,3 +37,76 @@
      "Common workflow language alternate entry point to allow cwl-runner 
 script as an implementation-agnostic script interpreter.") 
      (license license:asl2.0)))
+
+;; python-toil tightly integrates with cwltool using it as a library. So,
+;; create a library version of cwltool where inputs become propagated inputs.
+(define-public python-cwltool
+  (package
+    (inherit cwltool)
+    (name "python-cwltool")
+    (inputs
+     (list node))
+    (propagated-inputs
+     (modify-inputs (package-inputs cwltool)
+       (delete "node")))))
+
+(define-public python-toil
+  (package
+    (name "python-toil")
+    (version "6.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "toil" version))
+              (sha256
+               (base32
+                "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'disable-optional-features
+            (lambda _
+              (substitute* "requirements-cwl.txt"
+                ;; Loosen version restrictions on ruamel.yaml.
+                (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n")
+                ;; Remove optional dependency on galaxy-util and
+                ;; galaxy-tool-util. TODO: Package these and restore these
+                ;; dependencies.
+                (("galaxy-util[^\n]*") "")
+                (("galaxy-tool-util[^\n]*") ""))
+              ;; Disable optional wdl, wes and mesos features. We don't yet
+              ;; have dependencies packaged for them. TODO: Package these
+              ;; dependencies and enable these features.
+              (substitute* "setup.py"
+                (("\"wdl\",") "")
+                (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]")
+                 "toil-cwl-runner = toil.cwl.cwltoil:main")
+                (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "")
+                (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "")
+                (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") "")))))))
+    (propagated-inputs
+     (list python-addict
+           python-cachecontrol
+           python-configargparse
+           python-cwltool
+           python-dateutil
+           python-dill
+           python-docker
+           python-enlighten
+           python-psutil
+           python-pypubsub
+           python-pytz
+           python-pyyaml
+           python-requests
+           python-ruamel.yaml
+           python-typing-extensions-4.10
+           python-urllib3))
+    (home-page "https://github.com/DataBiosphere/toil")
+    (synopsis "Scalable, efficient and cross-platform workflow engine")
+    (description "Toil is a scalable, efficient, cross-platform pipeline
+management system, written entirely in Python, and designed around the
+principles of functional programming.")
+    (license (list license:asl2.0    ;; main license
+                   license:expat)))) ;; src/toil/batchSystems/lsf.py and
+                                     ;; src/toil/batchSystems/lsfHelper.py