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authorEfraim Flashner2023-03-22 13:25:19 +0200
committerEfraim Flashner2023-03-22 13:25:19 +0200
commit3cddd10e7b3a52d1d3f8411417e3b59a1ae558c9 (patch)
tree1d1387069e8b0b3cdee68dd6c76e3d170700652d
parent0bf0d2684677bc40c0759cb1640659bf03f882ae (diff)
downloadguix-bioinformatics-3cddd10e7b3a52d1d3f8411417e3b59a1ae558c9.tar.gz
bh20-seq-resource: Update to 1.0-4.2ae7191.
* gn/packages/bioinformatics.scm (bh20-seq-resource): Update to 1.0-4.2ae7191. [source]: Adjust snippet for changes in source. [arguments]: Skip tests. [propagated-inputs]: Add python-shexc-0.7. Remove python-dateutil, python-flask, python-pycurl, python38-ruaml.yaml-0.15.76, clustalw, python-twint. [native-inputs]: Remove git, python-oauth2client, python-uritemplate. Replace python-pytest-4 with python-pytest-5, python-pytest-runner-2 with python-pytest-runner-4.
-rw-r--r--gn/packages/bioinformatics.scm50
1 files changed, 24 insertions, 26 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index b58d97e..48f1c40 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1792,8 +1792,8 @@ suitable for long reads, but works also well with short reads.")
(license license:expat)))
(define-public bh20-seq-resource
- (let ((commit "ae4cb3c2cf7103bbc84f52618bb755d7ce25775b")
- (revision "3"))
+ (let ((commit "2ae71911cd87ce4f2eabdff21e538267b3270d45")
+ (revision "4"))
(package
(name "bh20-seq-resource")
(version (git-version "1.0" revision commit))
@@ -1804,36 +1804,34 @@ suitable for long reads, but works also well with short reads.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "1k0gsz4yc8l5znanzd094g2jp40ksbpa9667zr31ayrjx6labz02"))
+ (base32 "1k6cc88hrcm77jwpdk2084q0zirv2vlbz3c07nmpbhk1lhqk5x0n"))
(modules '((guix build utils)))
(snippet
'(begin
- (substitute* "setup.py"
- (("py-dateutil") "python-dateutil"))
- #t))))
+ (delete-file "gittaggers.py")))))
(build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #f)) ; Tests can't find pytest
(propagated-inputs
- `(("python-arvados-python-client" ,python-arvados-python-client)
- ("python-dateutil" ,python-dateutil)
- ("python-flask" ,python-flask)
- ("python-magic" ,python-magic)
- ("python-pyyaml" ,python-pyyaml)
- ("python-pycurl" ,python-pycurl)
- ("python-pyshex" ,python-pyshex)
- ("python-redis" ,python-redis)
- ("python-ruaml.yaml" ,python38-ruaml.yaml-0.15.76)
- ("clustalw" ,clustalw)
- ("python-schema-salad" ,python-schema-salad)
- ("python-twint" ,python-twint)
- ;; and for the service
- ("python" ,python)
- ("gunicorn" ,gunicorn)))
+ (list python-arvados-python-client
+ python-schema-salad
+ python-magic
+ python-pyshex
+ python-pyshexc-0.7
+ python-py-dateutil
+
+ ;; for the web
+ python-flask
+ python-pyyaml
+ python-redis
+
+ ;; and for the service
+ python
+ gunicorn))
(native-inputs
- `(("git" ,(@ (gnu packages version-control) git))
- ("python-oauth2client" ,python-oauth2client)
- ("python-pytest" ,python-pytest-4)
- ("python-pytest-runner" ,python-pytest-runner-2)
- ("python-uritemplate" ,python-uritemplate)))
+ (list python-pytest-4 ; < 6
+ python-pytest-runner-4)) ; < 5
(home-page "https://github.com/pubseq/bh20-seq-resource")
(synopsis
"Tool to upload SARS-CoV-19 sequences and service to kick off analysis")