diff options
| -rw-r--r-- | .guix-channel | 2 | ||||
| -rw-r--r-- | gn/packages/bioinformatics.scm | 14 | ||||
| -rw-r--r-- | gn/packages/crates-io.scm | 2 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 40 | ||||
| -rw-r--r-- | gn/packages/guile.scm | 21 |
5 files changed, 55 insertions, 24 deletions
diff --git a/.guix-channel b/.guix-channel index 3913b23..9c83b27 100644 --- a/.guix-channel +++ b/.guix-channel @@ -12,7 +12,7 @@ "3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5")))) (channel (name guix) - (url "https://git.savannah.gnu.org/git/guix.git") + (url "https://codeberg.org/guix/guix") (branch "master") (commit "61428ccf41f21f5ea1e4f1eec722ef9b1efc3a0e") (introduction diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 02c979d..4a85cff 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -56,6 +56,7 @@ #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) + #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) @@ -2339,14 +2340,14 @@ in-memory footprint at the cost of packing and unpacking.") (define-public vg (package (name "vg") - (version "1.61.0") + (version "1.65.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/vgteam/vg/releases/download/v" version "/vg-v" version ".tar.gz")) (sha256 - (base32 "1yb8ffqq65ma5di42qlj483x42viq5j4xyyg3vpww60gm15n1yxx")) + (base32 "022wiz0rs1x90nk9zaxcf8szhma8kzygnbfhciq9166kjysd0pc6")) (snippet #~(begin (use-modules (guix build utils)) @@ -2506,8 +2507,11 @@ in-memory footprint at the cost of packing and unpacking.") (substitute* "Makefile" ((".*test-docs.*") ""))))) (add-after 'build 'build-manpages - (lambda* (#:key inputs #:allow-other-keys) - (invoke "make" "man"))) + (lambda* (#:key make-flags #:allow-other-keys) + ;; vg is not in PATH. Replace it with full path. + (substitute* "doc/vgmanmd.py" + (("'vg'") "'./bin/vg'")) + (apply invoke "make" "man" make-flags))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -2527,9 +2531,11 @@ in-memory footprint at the cost of packing and unpacking.") bash-tap bc cmake-minimal + ghc-pandoc jq perl pkg-config + python samtools util-linux which diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 276b713..92969fd 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -19,7 +19,7 @@ (version "0.12.2") (source (origin (method url-fetch) - (uri (crate-uri "assert-cmd" version)) + (uri (crate-uri "assert_cmd" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index da514be..dce0301 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -116,7 +116,7 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "c0c6cc4110a5fe5c11b3a6994151ac9e807417dc") + (let ((commit "0976736c8efef8a8620e4713d8cdb0c25aad68a3") (revision "5")) (package (name "genenetwork3") @@ -130,7 +130,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1mhan38w68x5f9q285f4difd68bqz1ibvb54lfvx174i7wpn3gy7")))) + "1ks2ry5l2cfz97h03drdq6rlm518i5g4373nx5mx65gpxgrsdd77")))) (inputs (list python-click)) (native-inputs @@ -224,7 +224,7 @@ storage.") (license license:bsd-3))) (define-public genenetwork2 - (let ((commit "fd3de4e5f5ae6591b7718cf4d591feec66434611") + (let ((commit "fcde38b0f37f12508a01b16b7820029aa951bded") (revision "4")) (package (name "genenetwork2") @@ -237,7 +237,7 @@ storage.") (file-name (string-append name "-" version)) (sha256 (base32 - "15bz6dw8qg130ysa2k7lq6rd9s0y9c35bvwmr7i8zgk062vhzzxf")))) + "1rfg1x9wa4m5jfg4agvvwmzm217n79zggrig5r9jszx0bhl7y2qj")))) (native-inputs (list graphviz)) (propagated-inputs @@ -468,7 +468,7 @@ storage.") )))))) (define-public gn-uploader - (let ((commit "a675d462d2771f9e6c497c2385c985c2a6bb8806") + (let ((commit "b3b7973ffc36261dc6d79be17c85efbd79c317fa") (version "0.1.1")) (package (name "gn-uploader") @@ -483,25 +483,27 @@ storage.") (hash (content-hash (base32 - "0wa5ww43jimwgw9wvz5rmpxhva0fvbd5cqaf6m6d2d57v4klapsi"))))) + "1virv5ybvcs88qwl20593845hxkk7ax5mvjkxxj9a951cbk3pzpr"))))) (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 nss-certs + python-lxml python-redis python-flask python-pyyaml @@ -527,7 +529,7 @@ storage.") (license license:agpl3+)))) (define-public gn-auth - (let ((commit "aed581372c7c6b04023c85ce81943555cac363e6") + (let ((commit "09e27e96092f9a2e4f731709b8e8fdcd9835069a") (revision "01")) (package (name "gn-auth") @@ -542,7 +544,7 @@ storage.") (hash (content-hash (base32 - "138nb087h71xda87skl3cw7q8vcfc24yq7k08xv0kyjpcmwybsvq"))))) + "06hjsh6vgjmpsi2d8mzgigypykng7r0jdvvp15bs04ag83617i9k"))))) (build-system python-build-system) (arguments (list @@ -551,14 +553,15 @@ 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 @@ -580,8 +583,8 @@ storage.") (define-public gn-libs - (let ((commit "72a95f8ffa5401649f70978e863dd3f21900a611") - (revision "01")) + (let ((commit "8e4ebe14da610de84cd1f53eb491e7c50cd3d781") + (revision "02")) (package (name "gn-libs") (version (git-version "0.0.0" revision commit)) @@ -591,10 +594,11 @@ storage.") (uri (git-reference (url "https://git.genenetwork.org/gn-libs") (commit commit))) + (file-name (git-file-name name version)) (hash (content-hash (base32 - "1jvlz85pn10cx2icjxk0klz1g8k8vn1f8vp6kb4xyjskb1228yrx"))))) + "1qxnzp9ljjsk9jjf2q064n3mvwvn41xn3ay8iq1icilg3d9fqw82"))))) (build-system pyproject-build-system) (arguments (list diff --git a/gn/packages/guile.scm b/gn/packages/guile.scm index 3587b00..e95887c 100644 --- a/gn/packages/guile.scm +++ b/gn/packages/guile.scm @@ -197,25 +197,40 @@ for MySQL.") guile-redis guile-hashing guile-json-4)) + (scm-dev-path + (cons* + "./" + (map (lambda (x) (string-append x scm-dir)) + guile-inputs))) (scm-path (map (lambda (x) (string-append x scm-dir)) (cons* out guile-inputs))) (go-dir (string-append "/lib/guile/" effective "/site-ccache/")) + (go-dev-path + (map (lambda (x) (string-append x go-dir)) + guile-inputs)) (go-path (map (lambda (x) (string-append x go-dir)) (cons* out guile-inputs)))) (mkdir-p "bin") (copy-file "gn-guile.sh" "bin/gn-guile") + (copy-file "gn-guile.sh" "bin/gn-guile-dev") (copy-file "scripts/lmdb-publishdata-export.scm" "bin/lmdb-publishdata-export") (substitute* "bin/gn-guile" (("@SHELL@") bash) (("guile") guile) (("web/webserver.scm") webserver)) + (substitute* "bin/gn-guile-dev" + (("@SHELL@") bash) + (("guile") guile) + (("web/webserver.scm") "./web/webserver.scm")) (chmod "bin/gn-guile" #o755) + (chmod "bin/gn-guile-dev" #o755) (chmod "bin/lmdb-publishdata-export" #o755) (install-file "bin/gn-guile" bin) + (install-file "bin/gn-guile-dev" bin) (install-file "bin/lmdb-publishdata-export" bin) (wrap-script (string-append out "/bin/gn-guile") @@ -223,6 +238,12 @@ for MySQL.") `("GUILE_AUTO_COMPILE" ":" = ("0")) `("GUILE_LOAD_PATH" ":" prefix ,scm-path) `("GUILE_LOAD_COMPILED_PATH" ":" prefix ,go-path)) + (wrap-script + (string-append out "/bin/gn-guile-dev") + `("PATH" ":" prefix ,path) + `("GUILE_AUTO_COMPILE" ":" = ("0")) + `("GUILE_LOAD_PATH" ":" prefix ,scm-dev-path) + `("GUILE_LOAD_COMPILED_PATH" ":" prefix ,go-dev-path)) (wrap-program (string-append out "/bin/lmdb-publishdata-export") `("PATH" ":" prefix ,path) |