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-rw-r--r--gn/packages/bioinformatics.scm14
-rw-r--r--gn/packages/crates-io.scm2
-rw-r--r--gn/packages/genenetwork.scm40
-rw-r--r--gn/packages/guile.scm21
4 files changed, 54 insertions, 23 deletions
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)
generated by cgit v1.2.3 (git 2.47.1) at 2025-07-30 06:04:18 +0000