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-rw-r--r--gn/packages/genenetwork.scm144
1 files changed, 70 insertions, 74 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 91063b9..ce99066 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -130,50 +130,46 @@
(inputs
(list python-click))
(native-inputs
- `(("python-hypothesis" ,python-hypothesis)
- ("python-mypy" ,python-mypy)
- ("python-mypy-extensions" ,python-mypy-extensions)
- ("python-pylint" ,python-pylint)
- ("python-pytest" ,python-pytest)
- ("python-pytest-mock" ,python-pytest-mock)))
+ (list python-hypothesis
+ python-mypy
+ python-mypy-extensions
+ python-pylint
+ python-pytest
+ python-pytest-mock))
(propagated-inputs
- `(("gemma-wrapper" ,gemma-wrapper)
- ("python-wrapper" ,python-wrapper)
- ("csvdiff" ,csvdiff)
- ("gn-rust-correlation" ,gn-rust-correlation)
- ;; Replace use of bcrypt with argon below
- ("python-bcrypt" ,python-bcrypt)
- ("python-argon2-cffi" ,python-argon2-cffi)
- ("python-flask" ,python-flask)
- ("python-flask-cors" ,python-flask-cors)
- ;; Not working in Python > 3.8
- ;; python-ipfshttpclient
- ("python-lmdb" ,python-lmdb)
- ("python-mysqlclient" ,python-mysqlclient)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ;; python-pingouin << build failing
- ("python-pingouin-without-tests" ,python-pingouin-without-tests)
- ("python-plotly" ,python-plotly)
- ("python-pyld" ,python-pyld)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-pymonad" ,python-pymonad)
- ("python-redis" ,python-redis)
- ("python-requests" ,python-requests)
- ("python-scipy" ,python-scipy)
- ("python-authlib" ,python-authlib)
- ("python-sparqlwrapper" ,python-sparqlwrapper)
- ("python-email-validator" ,python-email-validator)
- ("python-xapian-bindings" ,python-xapian-bindings)
- ("python-biopython" ,python-biopython)
- ("r-optparse" ,r-optparse)
- ("r-qtl" ,r-qtl)
- ("r-rjson" ,r-rjson)
- ("r-stringi" ,r-stringi)
- ("r-wgcna" ,r-wgcna)
- ("r-ctl" ,r-ctl)
- ("rust-qtlreaper" ,rust-qtlreaper)
- ("diffutils" ,diffutils)))
+ (list gemma-wrapper
+ python-wrapper
+ csvdiff
+ gn-rust-correlation
+ python-bcrypt ;; Replace use of bcrypt with argon below
+ python-argon2-cffi
+ python-flask
+ python-flask-cors
+ python-lmdb
+ python-mysqlclient
+ python-numpy
+ python-pandas
+ python-pingouin-without-tests
+ python-plotly
+ python-pyld
+ python-scikit-learn
+ python-pymonad
+ python-redis
+ python-requests
+ python-scipy
+ python-authlib
+ python-sparqlwrapper
+ python-email-validator
+ python-xapian-bindings
+ python-biopython
+ r-optparse
+ r-qtl
+ r-rjson
+ r-stringi
+ r-wgcna
+ r-ctl
+ rust-qtlreaper
+ diffutils))
(build-system python-build-system)
(arguments
(list #:phases
@@ -273,7 +269,7 @@
javascript-plotly
javascript-typeahead
js-underscore
- javascript-uikit
+ javascript-uikit
js-smart-time-ago
javascript-nouislider
javascript-purescript-genome-browser
@@ -288,7 +284,7 @@
javascript-datatables-buttons-styles
javascript-shapiro-wilk
javascript-underscore-string
- javascript-htmx
+ javascript-htmx
javascript-qtip2
javascript-d3js
javascript-nvd3
@@ -297,8 +293,8 @@
javascript-zxcvbn
javascript-jquery-ui
javascript-jquery-cookie
- javascript-linkify
- javascript-linkify-html
+ javascript-linkify
+ javascript-linkify-html
; javascript-xterm -- disabled until we know what to do with it, not working on production
; javascript-xterm-style
; javascript-xterm-addon-fit
@@ -363,7 +359,7 @@
(define-public gn-uploader
(let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63")
- (version "0.0.1"))
+ (version "0.0.1"))
(package
(name "gn-uploader")
(version (string-append version "-" (string-take commit 8)))
@@ -371,33 +367,33 @@
(origin
(method git-fetch)
(uri (git-reference
- (url "https://git.genenetwork.org/gn-uploader")
- (commit commit)))
+ (url "https://git.genenetwork.org/gn-uploader")
+ (commit commit)))
(hash
- (content-hash
- (base32
- "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5")))))
+ (content-hash
+ (base32
+ "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5")))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-m" "unit_test")))))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-m" "unit_test")))))))
(native-inputs
(list python-mypy
- python-pylint
- python-pytest
- python-hypothesis))
+ python-pylint
+ python-pytest
+ python-hypothesis))
(propagated-inputs
(list gunicorn
- python-redis
- python-flask
- python-pyyaml
- python-jsonpickle
- python-mysqlclient))
+ python-redis
+ python-flask
+ python-pyyaml
+ python-jsonpickle
+ python-mysqlclient))
(synopsis "GeneNetwork Quality Control Application")
(description
"gn-uploader is a service allowing upload of new data into GeneNetwork,
@@ -414,21 +410,21 @@
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/genenetwork/gn-auth.git")
- (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f")))
+ (url "https://github.com/genenetwork/gn-auth.git")
+ (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f")))
(hash
- (content-hash
- (base32
- "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl")))))
+ (content-hash
+ (base32
+ "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl")))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-k" "unit_test")))))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-k" "unit_test")))))))
(native-inputs
(list python-hypothesis
python-mypy