diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 94 |
1 files changed, 45 insertions, 49 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 8ef0075..f8db089 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -19,12 +19,12 @@ #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages base) - #:use-module (gnu packages certs) + #:use-module ((gnu packages nss) #:select (nss-certs)) #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages check) #:use-module (gnu packages cran) - #:use-module (gnu packages crates-io) + #:use-module (past-crates packages crates-io) #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages ghostscript) @@ -40,6 +40,7 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages python-science) #:use-module (gnu packages rdf) #:use-module (gnu packages rust) #:use-module (gnu packages scheme) @@ -58,12 +59,12 @@ #:use-module (gn packages python) #:use-module (gn packages statistics) #:use-module (gn packages web) - #:use-module (gn packages python-web) - #:use-module (srfi srfi-1)) + #:use-module (srfi srfi-1) + #:use-module (gn packages databases)) (define-public rust-qtlreaper - (let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3") + (let ((commit "4dafa7289432d10685b6b235e3552ac3d681bb03") (revision "1")) (package (name "rust-qtlreaper") @@ -72,12 +73,12 @@ (origin (method git-fetch) (uri (git-reference - (url "https://github.com/chfi/rust-qtlreaper.git") + (url "https://github.com/genenetwork/rust-qtlreaper.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "0h70aalsplmc6xn1w7ha102n3bsi3gqkbnbrjvjm2za37c07gv0g")))) + "1p7dmxh43ly0k7q6va0lzisqnk1i7af3dy5aw1sr4y5s7z0h6i0y")))) (build-system cargo-build-system) (arguments `(#:cargo-inputs @@ -101,7 +102,7 @@ (("-0.3223330030526561") "-0.32233300305265566")) (assoc-ref %standard-phases 'check))) #t))))) - (home-page "https://github.com/chfi/rust-qtlreaper") + (home-page "https://github.com/genenetwork/rust-qtlreaper") (synopsis "Reimplementation of genenetwork/QTLReaper in Rust") (description "Reimplementation of genenetwork/QTLReaper in Rust") (license #f)))) @@ -116,7 +117,7 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "757fce9fc0e08941983113157edaf6e1d552aebd") + (let ((commit "e6c44577b2489f7b1523cb6a5fd332015bde25c5") (revision "5")) (package (name "genenetwork3") @@ -130,7 +131,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0d5qfxr4hmkqs8g0ddc26iylrd2b9rcigyhar6gpjcghgdlkmzv4")))) + "0i2n46lg73w06dfqcs4sxvwwfdxa0536gv95ism85h4j3dm9vzhz")))) (inputs (list python-click)) (native-inputs @@ -146,15 +147,15 @@ nss-certs gemma-wrapper gn-rust-correlation + gunicorn python-argon2-cffi python-authlib - python-bcrypt ;; Replace use of bcrypt with argon python-biopython python-email-validator python-flask python-flask-cors python-lmdb - python-mysqlclient + python-mysqlclient-2.2.7 python-numpy python-pandas python-pingouin-without-tests @@ -168,6 +169,7 @@ python-scikit-learn python-scipy python-sparqlwrapper + python-structlog python-wrapper python-xapian-bindings r @@ -178,6 +180,7 @@ r-rjson r-stringi r-wgcna + r-thor rust-qtlreaper)) (build-system python-build-system) (arguments @@ -224,7 +227,7 @@ storage.") (license license:bsd-3))) (define-public genenetwork2 - (let ((commit "a055ddf972f274436118def31e68dee520f88fbb") + (let ((commit "5e596f0814b4cad57a847fae03df2867b6327653") (revision "4")) (package (name "genenetwork2") @@ -237,7 +240,7 @@ storage.") (file-name (string-append name "-" version)) (sha256 (base32 - "0f3myldadsf24s5ll12z08yxlj0q2kgb96jx7mcjndc7m4cxmwgs")))) + "1arnq4b7c6i6fnvfim3yyghrvr0ncjdp1a4ix1hgj9bz2r9vxnzi")))) (native-inputs (list graphviz)) (propagated-inputs @@ -326,7 +329,7 @@ storage.") python-lxml python-markdown python-mypy - python-mysqlclient + python-mysqlclient-2.2.7 python-numpy python-pandas python-pylint @@ -336,13 +339,15 @@ storage.") python-rdflib python-redis python-requests - python-rpy2 + ;; python-rpy2 ; restore once python-rpy2 dependencies get upstream + python-rpy2-patched ; remove this once python-rpy2 is fixed upstream python-scipy python-setuptools python-simplejson python-wrapper python-xlsxwriter python-pillow-9 + python-structlog r r-ctl r-qtl @@ -375,21 +380,6 @@ storage.") (("\\./gn2/wqflask/static/gif/error") (string-append (site-packages inputs outputs) "/gn2/wqflask/static/gif/error"))))) - (add-after 'unpack 'fix-paths-scripts - (lambda _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python3") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))))) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) @@ -468,7 +458,7 @@ storage.") )))))) (define-public gn-uploader - (let ((commit "a675d462d2771f9e6c497c2385c985c2a6bb8806") + (let ((commit "c4494da2e81780bbeeac8936d1fe1aede01cf73c") (version "0.1.1")) (package (name "gn-uploader") @@ -483,21 +473,22 @@ storage.") (hash (content-hash (base32 - "0wa5ww43jimwgw9wvz5rmpxhva0fvbd5cqaf6m6d2d57v4klapsi"))))) + "0fhhpvxaj0anh21pqabikv5wmd1cj3nx2j1bcd9ld8q3ykmm8a9s"))))) (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" "-n" "auto"))))))) (native-inputs (list python-mypy python-pylint python-pytest - python-hypothesis)) + python-hypothesis + python-pytest-xdist)) (propagated-inputs (list gn-libs gunicorn @@ -509,7 +500,7 @@ storage.") python-authlib python-pymonad python-jsonpickle - python-mysqlclient + python-mysqlclient-2.2.7 ;;python-flask-session temporary-python-flask-session web-bootstrap-5 @@ -518,7 +509,8 @@ storage.") javascript-datatables-select javascript-datatables-buttons-3 javascript-datatables-scroller-2 - node-resumablejs)) + node-resumablejs + rust-qtlreaper)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, @@ -528,7 +520,7 @@ storage.") (license license:agpl3+)))) (define-public gn-auth - (let ((commit "aed581372c7c6b04023c85ce81943555cac363e6") + (let ((commit "9839e5bf35bd7be158b35fa98a734f7a3473688d") (revision "01")) (package (name "gn-auth") @@ -543,7 +535,7 @@ storage.") (hash (content-hash (base32 - "138nb087h71xda87skl3cw7q8vcfc24yq7k08xv0kyjpcmwybsvq"))))) + "1lsi7z8hvpdqgcsx3zc5ip701xka9s75c7r4pjlby2ryjc0gw83d"))))) (build-system python-build-system) (arguments (list @@ -552,14 +544,15 @@ storage.") (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? - (invoke "pytest" "-k" "unit_test"))))))) + (invoke "pytest" "-m" "unit_test" "-n" "auto"))))))) (native-inputs (list python-hypothesis python-mypy python-mypy-extensions python-pylint python-pytest - python-pytest-mock)) + python-pytest-mock + python-pytest-xdist)) (propagated-inputs (list gn-libs gunicorn @@ -570,9 +563,10 @@ storage.") python-email-validator python-flask python-flask-cors - python-mysqlclient + python-mysqlclient-2.2.7 python-pymonad python-redis + python-structlog yoyo-migrations)) (home-page "https://github.com/genenetwork/gn-auth") (synopsis "Authentication and Authorisation server for GeneNetwork services") @@ -581,8 +575,8 @@ storage.") (define-public gn-libs - (let ((commit "27425e6d57634106d2991ad17414d45c490c931c") - (revision "01")) + (let ((commit "9422e39e5b79a4aaca7dc368368d39141a0242b7") + (revision "02")) (package (name "gn-libs") (version (git-version "0.0.0" revision commit)) @@ -592,10 +586,11 @@ storage.") (uri (git-reference (url "https://git.genenetwork.org/gn-libs") (commit commit))) + (file-name (git-file-name name version)) (hash (content-hash (base32 - "1pljmgy60qppncx6dmyf8cdsjnf12rcwmismd40rl6vsyna7msk5"))))) + "03i1kj7jbmlkjs61a9fb4j3s78p4d5lmd8lqnfsv42wxwwyvsm8p"))))) (build-system pyproject-build-system) (arguments (list @@ -615,7 +610,8 @@ storage.") (list python-authlib python-pymonad python-requests - python-mysqlclient)) + python-structlog + python-mysqlclient-2.2.7)) (home-page "https://github.com/genenetwork/gn-libs") (synopsis "Tools/utilities for GeneNetwork projects.") (description "A collection of tools and utilities used across multiple |