gnu: Move all snakemake variants to python-science.

* gnu/packages/python-xyz.scm (snakemake-5, snakemake-6, snakemake-7):
Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: Ia771b316049f375183025e7617e6d0ddf06f99ff

1 files changed, 271 insertions, 0 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 7792e51e30..376ae67570 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -5004,6 +5004,277 @@ providing a clean and modern domain specific specification language (DSL) in
 Python style, together with a fast and comfortable execution environment.")
     (license license:expat)))
 
+(define-public snakemake-5
+  (package
+    (name "snakemake")
+    (version "5.32.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list
+        ;; We have no TES support.
+        "--ignore=tests/test_tes.py"
+        ;; This test attempts to change S3 buckets on AWS and fails
+        ;; because there are no AWS credentials.
+        "--ignore=tests/test_tibanna.py"
+        ;; It's a similar story with this test, which requires access
+        ;; to the Google Storage service.
+        "--ignore=tests/test_google_lifesciences.py"
+        ;; Unclear failure.
+        "-k" "not test_lint[long_run-positive]")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'tabulate-compatibility
+            (lambda _
+              (substitute* "snakemake/dag.py"
+                (("\"job\": rule,")
+                 "\"job\": rule.name,"))))
+          (add-after 'unpack 'patch-version
+            (lambda _
+              (substitute* "setup.py"
+                (("version=versioneer.get_version\\(\\)")
+                 (format #f "version=~s" #$version)))
+              (substitute* '("snakemake/_version.py"
+                             "versioneer.py")
+                (("0\\+unknown") #$version))))
+          ;; For cluster execution Snakemake will call Python.  Since there is
+          ;; no suitable PYTHONPATH set, cluster execution will fail.  We fix
+          ;; this by calling the snakemake wrapper instead.
+          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+            (lambda _
+              (substitute* "snakemake/executors/__init__.py"
+                (("\\{sys.executable\\} -m snakemake")
+                 (string-append #$output "/bin/snakemake")))))
+          (add-before 'check 'pre-check
+            (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-appdirs
+           python-configargparse
+           python-datrie
+           python-docutils
+           python-gitpython
+           python-jinja2
+           python-jsonschema
+           python-nbformat
+           python-networkx
+           python-psutil
+           python-pulp
+           python-pyyaml
+           python-ratelimiter
+           python-requests
+           python-toposort
+           python-wrapt))
+    (native-inputs
+     (list git-minimal
+           python-wrapper
+           python-pytest
+           python-pandas
+           python-requests-mock
+           python-setuptools
+           python-wheel))
+    (home-page "https://snakemake.readthedocs.io")
+    (synopsis "Python-based execution environment for make-like workflows")
+    (description
+      "Snakemake aims to reduce the complexity of creating workflows by
+providing a clean and modern domain specific specification language (DSL) in
+Python style, together with a fast and comfortable execution environment.")
+    (license license:expat)))
+
+(define-public snakemake-6
+  (package
+    (inherit snakemake-5)
+    (name "snakemake")
+    (version "6.15.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list
+        ;; This test attempts to change S3 buckets on AWS and fails
+        ;; because there are no AWS credentials.
+        "--ignore=tests/test_tibanna.py"
+        ;; Unclear failure.
+        "-k" "not test_lint[long_run-positive]")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; For cluster execution Snakemake will call Python.  Since there is
+          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
+          ;; fix this by calling the snakemake wrapper instead.
+
+          ;; XXX: There is another instance of sys.executable on line 692, but
+          ;; it is not clear how to patch it.
+          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+            (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* "snakemake/executors/__init__.py"
+                (("\\{sys.executable\\} -m snakemake")
+                 (string-append #$output "/bin/snakemake")))))
+          (add-after 'unpack 'tabulate-compatibility
+            (lambda _
+              (substitute* "snakemake/dag.py"
+                (("\"job\": rule,")
+                 "\"job\": rule.name,"))))
+          (add-after 'unpack 'patch-version
+            (lambda _
+              (substitute* "setup.py"
+                (("version=versioneer.get_version\\(\\)")
+                 (format #f "version=~s" #$version)))
+              (substitute* '("snakemake/_version.py"
+                             "versioneer.py")
+                (("0\\+unknown") #$version))))
+          (add-before 'check 'pre-check
+            (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-appdirs
+           python-configargparse
+           python-connection-pool
+           python-datrie
+           python-docutils
+           python-filelock
+           python-gitpython
+           python-jinja2
+           python-jsonschema
+           python-nbformat
+           python-networkx
+           python-psutil
+           python-pulp
+           python-pyyaml
+           python-py-tes
+           python-ratelimiter
+           python-requests
+           python-smart-open
+           python-stopit
+           python-tabulate
+           python-toposort
+           python-wrapt))
+    (native-inputs
+     (list git-minimal
+           python-wrapper
+           python-pytest
+           python-pandas
+           python-requests-mock
+           python-setuptools
+           python-wheel))))
+
+(define-public snakemake-7
+  (package
+    (inherit snakemake-6)
+    (name "snakemake")
+    (version "7.32.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; This test attempts to change S3 buckets on AWS and fails
+      ;; because there are no AWS credentials.
+      '(list "--ignore=tests/test_tibanna.py"
+             ;; It's a similar story with this test, which requires access to
+             ;; the Google Storage service.
+             "--ignore=tests/test_google_lifesciences.py"
+             "--ignore-glob=tests/test_conda_python_3_7_script/*"
+             ;; We don't have a slurm installation in the build environment
+             "--ignore=tests/test_slurm.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; For cluster execution Snakemake will call Python.  Since there is
+          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
+          ;; fix this by calling the snakemake wrapper instead.
+          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+            (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* "snakemake/executors/__init__.py"
+                (("self\\.get_python_executable\\(\\),")
+                 "")
+                (("\"-m snakemake\"")
+                 (string-append "\"" #$output
+                                "/bin/snakemake" "\""))
+                ;; The snakemake command produced by format_job_exec contains
+                ;; references to /gnu/store.  Prior to patching above that's
+                ;; just a reference to Python; after patching it's a reference
+                ;; to the snakemake executable.
+                ;;
+                ;; In Tibanna execution mode Snakemake arranges for a certain
+                ;; Docker image to be deployed to AWS.  It then passes its own
+                ;; command line to Tibanna.  This is misguided because it only
+                ;; ever works if the local Snakemake command was run inside
+                ;; the same Docker image.  In the case of using Guix this is
+                ;; never correct, so we need to replace the store reference.
+                (("tibanna_args.command = command")
+                 (string-append
+                  "tibanna_args.command = command.replace('"
+                  #$output "/bin/snakemake', 'python3 -m snakemake')")))))
+          (add-after 'unpack 'patch-version
+            (lambda _
+              (substitute* "setup.py"
+                (("version=versioneer.get_version\\(\\)")
+                 (format #f "version=~s" #$version)))
+              (substitute* '("snakemake/_version.py"
+                             "versioneer.py")
+                (("0\\+unknown") #$version))))
+          (add-before 'check 'pre-check
+            (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-appdirs
+           python-configargparse
+           python-connection-pool
+           python-datrie
+           python-docutils
+           python-filelock
+           python-gitpython
+           python-humanfriendly
+           python-jinja2
+           python-jsonschema
+           python-nbformat
+           python-networkx
+           python-psutil
+           python-pulp
+           python-pyyaml
+           python-py-tes
+           python-requests
+           python-retry
+           python-reretry
+           python-smart-open
+           python-stopit
+           python-tabulate
+           python-throttler
+           python-toposort
+           python-wrapt
+           python-yte))
+    (native-inputs
+     (list git-minimal
+           python-wrapper
+           python-pytest
+           python-pandas
+           python-requests-mock
+           python-setuptools
+           python-wheel))))
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar