Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics

6 files changed, 116 insertions, 462 deletions

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 55f7355..c9c7a87 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -4,93 +4,11 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
-  #:use-module (guix build-system cargo))
+  #:use-module (guix build-system cargo)
+  #:use-module (gnu packages crates-io))
 
 ;; Please keep these packages sorted alphabetically
 
-(define-public rust-crossbeam-deque-0.2
-  (package
-    (name "rust-crossbeam-deque")
-    (version "0.2.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "crossbeam-deque" version))
-        (file-name (string-append name "-" version ".crate"))
-        (sha256
-         (base32
-          "1wwwbnvxh0rza38xiws8qc46klzhv19zgvarn37pijis6v2zhfgp"))))
-    (build-system cargo-build-system)
-    (home-page "https://github.com/crossbeam-rs/crossbeam/tree/master/crossbeam-deque")
-    (synopsis "Concurrent work-stealing deque")
-    (description "Concurrent work-stealing deque")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
-(define-public rust-crossbeam-epoch-0.3
-  (package
-    (name "rust-crossbeam-epoch")
-    (version "0.3.1")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "crossbeam-epoch" version))
-        (file-name
-          (string-append name "-" version ".crate"))
-        (sha256
-         (base32
-          "0l4igvp2i7b6dgaiq040j8kj8hygwdpr6ppzh1hrbsbx83sj2wcj"))))
-      (build-system cargo-build-system)
-    (home-page "https://github.com/crossbeam-rs/crossbeam/tree/master/crossbeam-epoch")
-    (synopsis "Epoch-based garbage collection")
-    (description "Epoch-based garbage collection")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
-(define-public rust-crossbeam-utils-0.2
-  (package
-    (name "rust-crossbeam-utils")
-    (version "0.2.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "crossbeam-utils" version))
-        (file-name (string-append name "-" version ".crate"))
-        (sha256
-         (base32
-          "1n8qr52sw9y6yxzyfxi1phh55rsxms7ry4iipdd8vmd16ag8jq17"))))
-      (build-system cargo-build-system)
-    (home-page "https://github.com/crossbeam-rs/crossbeam/tree/master/crossbeam-utils")
-    (synopsis "Utilities for concurrent programming")
-    (description
-      "Utilities for concurrent programming")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
-(define-public rust-heck-0.3
-  (package
-    (name "rust-heck")
-    (version "0.3.1")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "heck" version))
-        (file-name (string-append name "-" version ".crate"))
-        (sha256
-         (base32
-          "01a2v7yvkiqxakdqz4hw3w3g4sm52ivz9cs3qcsv2arxsmw4wmi0"))))
-    (build-system cargo-build-system)
-    (home-page "https://github.com/withoutboats/heck")
-    (synopsis "heck is a case conversion library.")
-    (description
-      "heck is a case conversion library.")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
 (define-public rust-itertools-0.7
   (package
     (name "rust-itertools")
@@ -104,31 +22,18 @@
          (base32
           "03cpsj26xmyamcalclqzr1i700vwx8hnbgxbpjvs354f8mnr8iqd"))))
     (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-either" ,rust-either-1.5))
+       #:cargo-development-inputs
+       (("rust-permutohedron" ,rust-permutohedron-0.2)
+        ("rust-quickcheck" ,rust-quickcheck-0.5))))
     (home-page "https://github.com/rust-itertools/itertools")
     (synopsis
-      "Extra iterator adaptors, iterator methods, free functions, and macros.")
+     "Extra iterator adaptors, iterator methods, free functions, and macros")
     (description
-      "Extra iterator adaptors, iterator methods, free functions, and macros.")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
-(define-public rust-matrixmultiply-0.1
-  (package
-    (name "rust-matrixmultiply")
-    (version "0.1.15")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "matrixmultiply" version))
-        (file-name (string-append name "-" version ".crate"))
-        (sha256
-         (base32
-          "00p0fpjhm45qdzi37mgv7ggsy8b9gqvq4999yrbgyn1dxkf6gbfw"))))
-    (build-system cargo-build-system)
-    (home-page "https://github.com/bluss/matrixmultiply/")
-    (synopsis "General matrix multiplication for f32 and f64 matrices.")
-    (description "General matrix multiplication for f32 and f64 matrices. Operates on matrices with general layout (they can use arbitrary row and column stride). Detects and uses AVX or SSE2 on x86 platforms transparently for higher performance. Uses a microkernel strategy, so that the implementation is easy to parallelize and optimize.")
+     "Extra iterator adaptors, iterator methods, free functions, and macros.")
     (properties '((hidden? . #t)))
     (license (list license:asl2.0
                    license:expat))))
@@ -146,53 +51,25 @@
          (base32
           "0a5rfwcbqnvbwi3nw5sfz6kf0flhmjxs64s0b4kxc6lhmyl81wvw"))))
     (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-itertools" ,rust-itertools-0.7)
+        ("rust-matrixmultiply" ,rust-matrixmultiply-0.1)
+        ("rust-num-complex" ,rust-num-complex-0.2)
+        ;("rust-blas-src" ,rust-blas-src-0.2)
+        ;("rust-cblas-src" ,rust-cblas-src-0.1)
+        ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
+        ("rust-serde" ,rust-serde-1.0))
+       #:cargo-development-inputs
+       (("rust-defmac" ,rust-defmac-0.1)
+        ("rust-quickcheck" ,rust-quickcheck-0.7)
+        ("rust-rawpointer" ,rust-rawpointer-0.1))))
     (home-page "https://github.com/rust-ndarray/ndarray")
     (synopsis
-      "ndarray implements an n-dimensional container for general elements and for numerics.")
+     "ndarray implements an n-dimensional container for general elements and for numerics")
     (description
-      "ndarray implements an n-dimensional container for general elements and for numerics.")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
-(define-public rust-rayon-1.0
-  (package
-    (name "rust-rayon")
-    (version "1.0.3")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "rayon" version))
-        (file-name (string-append name "-" version ".crate"))
-        (sha256
-        (base32
-        "0wq41f15y05nlarijn9c1vxscxj5sazn3lhd6mmnicj5fzr18f1p"))))
-    (build-system cargo-build-system)
-    (home-page "https://github.com/rayon-rs/rayon")
-    (synopsis
-      "Simple work-stealing parallelism for Rust")
-    (description
-      "Simple work-stealing parallelism for Rust")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
-(define-public rust-rayon-core-1.4
-  (package
-    (name "rust-rayon-core")
-    (version "1.4.1")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "rayon-core" version))
-        (file-name (string-append name "-" version ".crate"))
-        (sha256
-         (base32
-          "0mkkabm3h4xvrkvjp675c07zcpcb7jk09rlg9mbpfs5s5blx2mdh"))))
-    (build-system cargo-build-system)
-    (home-page "https://github.com/rayon-rs/rayon")
-    (synopsis "Core APIs for Rayon")
-    (description "Core APIs for Rayon")
+     "ndarray implements an n-dimensional container for general elements and for numerics.")
     (properties '((hidden? . #t)))
     (license (list license:asl2.0
                    license:expat))))
@@ -210,11 +87,15 @@
          (base32
           "1mvfv1l8vp3y402fkl2wcl34hi7gmr4bqha13dfz2xf3kjzwvhhn"))))
     (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-structopt-derive" ,rust-structopt-derive-0.2))))
     (home-page "https://github.com/TeXitoi/structopt")
-    (synopsis
-      "Parse command line argument by defining a struct.")
+    (synopsis "Parse command line arguments by defining a struct")
     (description
-      "Parse command line argument by defining a struct.")
+     "Parse command line arguments by defining a struct.")
     (properties '((hidden? . #t)))
     (license (list license:asl2.0
                    license:expat))))
@@ -232,33 +113,18 @@
          (base32
           "01sis9z5kqmyhvzbnmlzpdxcry99a0b9blypksgnhdsbm1hh40ak"))))
     (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-heck" ,rust-heck-0.3)
+        ("rust-proc-macro2" ,rust-proc-macro2-0.4)
+        ("rust-quote" ,rust-quote-0.6)
+        ("rust-syn" ,rust-syn-0.15))))
     (home-page "https://github.com/TeXitoi/structopt")
     (synopsis
-      "Parse command line argument by defining a struct, derive crate.")
-    (description
-      "Parse command line argument by defining a struct, derive crate.")
-    (properties '((hidden? . #t)))
-    (license (list license:asl2.0
-                   license:expat))))
-
-(define-public rust-unicode-segmentation-1.6
-  (package
-    (name "rust-unicode-segmentation")
-    (version "1.6.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "unicode-segmentation" version))
-        (file-name (string-append name "-" version ".crate"))
-        (sha256
-         (base32
-          "1h7d48mzpi8hwf5cvnq07warkv86pvapzzzf32hvbjsk20yiagp8"))))
-    (build-system cargo-build-system)
-    (home-page "https://github.com/unicode-rs/unicode-segmentation")
-    (synopsis "Grapheme Cluster, Word and Sentence boundaries for rust")
+     "Parse command line argument by defining a struct, derive crate")
     (description
-     "This crate provides Grapheme Cluster, Word and Sentence boundaries
-according to Unicode Standard Annex #29 rules.")
+     "Parse command line argument by defining a struct, derive crate.")
     (properties '((hidden? . #t)))
     (license (list license:asl2.0
                    license:expat))))
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 84251a4..6e0c909 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -13,6 +13,7 @@
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages time)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages xml)
   #:use-module (gn packages python)
   #:use-module (guix download)
   #:use-module (guix packages)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 489a88f..232e4f7 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -27,6 +27,7 @@
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
   #:use-module (gn packages bioinformatics)
   #:use-module (gn packages crates-io)
   #:use-module (gn packages elixir)
@@ -205,83 +206,23 @@ location of a putative QTL.")
        `(#:cargo-inputs
          (("rust-rand" ,rust-rand-0.6)
           ("rust-structopt" ,rust-structopt-0.2)
-          ("rust-rayon" ,rust-rayon-1.0)
+          ("rust-rayon" ,rust-rayon-1.3)
           ("rust-serde" ,rust-serde-1.0)
           ("rust-serde-json" ,rust-serde-json-1.0)
           ("rust-ndarray" ,rust-ndarray-0.12))
-         #:cargo-development-inputs
-         (("rust-ansi-term" ,rust-ansi-term-0.11)
-          ("rust-arrayvec" ,rust-arrayvec-0.4)
-          ("rust-atty" ,rust-atty-0.2)
-          ("rust-autocfg" ,rust-autocfg-0.1)
-          ("rust-bitflags" ,rust-bitflags-1)
-          ("rust-cfg-if" ,rust-cfg-if-0.1)
-          ("rust-clap" ,rust-clap-2)
-          ("rust-cloudabi" ,rust-cloudabi-0.0)
-          ("rust-crossbeam-deque" ,rust-crossbeam-deque-0.2)
-          ("rust-crossbeam-epoch" ,rust-crossbeam-epoch-0.3)
-          ("rust-crossbeam-utils" ,rust-crossbeam-utils-0.2)
-          ("rust-either" ,rust-either-1.5)
-          ("rust-fuchsia-cprng" ,rust-fuchsia-cprng-0.1)
-          ("rust-heck" ,rust-heck-0.3)
-          ("rust-itertools" ,rust-itertools-0.7)
-          ("rust-itoa" ,rust-itoa-0.4)
-          ("rust-lazy-static" ,rust-lazy-static-1.3)
-          ("rust-libc" ,rust-libc-0.2)
-          ("rust-maxtrixmultiply" ,rust-matrixmultiply-0.1)
-          ("rust-memoffset" ,rust-memoffset-0.2)
-          ("rust-nodrop" ,rust-nodrop-0.1)
-          ("rust-num-complex" ,rust-num-complex-0.2)
-          ("rust-num-cpus" ,rust-num-cpus-1.10)
-          ("rust-num-traits" ,rust-num-traits-0.2)
-          ("rust-numtoa" ,rust-numtoa-0.1)
-          ("rust-proc-macro2" ,rust-proc-macro2-1.0)
-          ("rust-proc-macro2" ,rust-proc-macro2-0.4)
-          ("rust-quote" ,rust-quote-1.0)
-          ("rust-quote" ,rust-quote-0.6)
-          ("rust-rand" ,rust-rand-0.6)
-          ("rust-rand-chacha" ,rust-rand-chacha-0.1)
-          ("rust-rand-core" ,rust-rand-core-0.3)
-          ("rust-rand-hc" ,rust-rand-hc-0.1)
-          ("rust-rand-isaac" ,rust-rand-isaac-0.1)
-          ("rust-rand-jitter" ,rust-rand-jitter-0.1)
-          ("rust-rand-os" ,rust-rand-os-0.1)
-          ("rust-rand-pcg" ,rust-rand-pcg-0.1)
-          ("rust-rand-xorshift" ,rust-rand-xorshift-0.1)
-          ("rust-rawpointer" ,rust-rawpointer-0.1)
-          ("rust-rayon" ,rust-rayon-1.0)
-          ("rust-rayon-core" ,rust-rayon-core-1.4)
-          ("rust-rdrand" ,rust-rdrand-0.4)
-          ("rust-redox-syscall" ,rust-redox-syscall-0.1)
-          ("rust-redox-termios" ,rust-redox-termios-0.1)
-          ("rust-ryu" ,rust-ryu-1.0)
-          ("rust-scopeguard" ,rust-scopeguard-0.3)
-          ("rust-serde" ,rust-serde-1.0)
-          ("rust-serde-derive" ,rust-serde-derive-1.0)
-          ("rust-serde-json" ,rust-serde-json-1.0)
-          ("rust-strsim" ,rust-strsim-0.8)
-          ("rust-structopt" ,rust-structopt-0.2)
-          ("rust-structopt-derive" ,rust-structopt-derive-0.2)
-          ("rust-syn" ,rust-syn-1.0)
-          ("rust-syn" ,rust-syn-0.15)
-          ("rust-termion" ,rust-termion-1.5)
-          ("rust-textwrap" ,rust-textwrap-0.11)
-          ("rust-unicode-segmentation" ,rust-unicode-segmentation-1.6)
-          ("rust-unicode-width" ,rust-unicode-width-0.1)
-          ("rust-unicode-xid" ,rust-unicode-xid-0.2)
-          ("rust-unicode-xid" ,rust-unicode-xid-0.1)
-          ("rust-vec-map" ,rust-vec-map-0.8)
-          ("rust-winapi" ,rust-winapi-0.3))
-         #:tests? #f ; Test results vary based on the machine running them.
          #:phases
          (modify-phases %standard-phases
-           (add-after 'unpack 'update-test-data
+           ;; Test results vary based on the machine running them.
+           (replace 'check
              (lambda _
-               (substitute* "src/geneobject.rs"
-                 ;; array![Genotype::Unk, Genotype::Unk, Genotype::Pat]
-                 (("0.3421367343627405") "0.3421367343627406")
-                 ;; array![Genotype::Unk, Genotype::Unk, Genotype::Unk]
-                 (("-0.3223330030526561") "-0.32233300305265566"))
+               (or (assoc-ref %standard-phases 'check)
+                   (begin
+                     (substitute* "src/geneobject.rs"
+                       ;; array![Genotype::Unk, Genotype::Unk, Genotype::Pat]
+                       (("0.3421367343627405") "0.3421367343627406")
+                       ;; array![Genotype::Unk, Genotype::Unk, Genotype::Unk]
+                       (("-0.3223330030526561") "-0.32233300305265566"))
+                     (assoc-ref %standard-phases 'check)))
                #t)))))
       (home-page "https://github.com/chfi/rust-qtlreaper")
       (synopsis "Reimplementation of genenetwork/QTLReaper in Rust")
diff --git a/gn/packages/node.scm b/gn/packages/node.scm
index d83714d..18512bf 100644
--- a/gn/packages/node.scm
+++ b/gn/packages/node.scm
@@ -4,7 +4,8 @@
   #:use-module (guix packages)
   #:use-module (guix git-download)
   #:use-module (guix build-system node)
-  #:use-module (gnu packages lisp-xyz))
+  #:use-module (gnu packages lisp-xyz)
+  #:use-module (gnu packages node-xyz))
 
 (define-public node-asap
   (package
@@ -327,29 +328,6 @@ Google Maps, and others.")
     (description "Plain color conversion functions in JavaScript.")
     (license license:expat)))
 
-(define-public node-color-name
-  (package
-    (name "node-color-name")
-    (version "1.1.3")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/colorjs/color-name")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "09rbmj16nfwcwkhrybqxyy66bkrs50vpw6hkdqqb14l3gsyxpr74"))))
-    (build-system node-build-system)
-    (arguments '(#:tests? #f))
-    ;(native-inputs
-    ; `(("node-assert" ,node-assert)))
-    (home-page "https://github.com/colorjs/color-name")
-    (synopsis "A JSON with CSS color names")
-    (description "A JSON with CSS color names.")
-    (license license:expat)))
-
 (define-public node-color-string
   (package
     (name "node-color-string")
@@ -703,27 +681,6 @@ functionality to JupyterHub deployments.")
     (description "Check if a certain flag is enabled.")
     (license license:expat)))
 
-(define-public node-env-variable
-  (package
-    (name "node-env-variable")
-    (version "0.0.4")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/bigpipe/env-variable")
-               (commit version)))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "0nnpxjxfhy4na7fixb7p3ww6ard5xgggfm83b78i333867r4gmsq"))))
-    (build-system node-build-system)
-    (arguments '(#:tests? #f)) ; No tests.
-    (home-page "https://github.com/bigpipe/env-variable")
-    (synopsis "Cross platform environment variables with process.env, window.name, location.hash and localStorage fallbacks")
-    (description "Cross platform environment variables with process.env, window.name, location.hash and localStorage fallbacks.")
-    (license license:expat)))
-
 (define-public node-eventemitter3
   (package
     (name "node-eventemitter3")
@@ -768,34 +725,6 @@ are some slight differences:
 @end itemize")
     (license license:expat)))
 
-(define-public node-far
-  (package
-    (name "node-far")
-    (version "0.0.7")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/felixge/node-far")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "083rv1rszjn0i91zcpaghlid0kwhk0angmpj4hiflrlyhd6cmjzw"))))
-    (build-system node-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (invoke "bin/node-far" "tests/"))))))
-    (inputs
-     `(("node-oop" ,node-oop)))
-    (home-page "https://github.com/felixge/node-far")
-    (synopsis "Node.js test runner")
-    (description "A simple test runner that finds and runs multiple node.js files, while providing useful information about output and exit codes.")
-    (license license:expat)))
-
 (define-public node-fast-safe-stringify
   (package
     (name "node-fast-safe-stringify")
@@ -1185,27 +1114,6 @@ such as reverse proxies and load balancers.")
     (description "A mutable object format designed for chaining & objectMode streams.")
     (license license:expat)))
 
-(define-public node-long-stack-traces
-  (package
-    (name "node-long-stack-traces")
-    (version "0.1.2")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/tlrobinson/long-stack-traces")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "0famwsyc6xawi30v25zi65d8fhbvlvh976bqydf1dqn5gz200cl3"))))
-    (build-system node-build-system)
-    (arguments '(#:tests? #f)) ; No tests.
-    (home-page "https://github.com/tlrobinson/long-stack-traces")
-    (synopsis "Long stacktraces for V8 implemented in user-land JavaScript")
-    (description "Long stacktraces for V8 implemented in user-land JavaScript.")
-    (license license:expat))) ; in README
-
 (define-public node-lynx
   (package
     (name "node-lynx")
@@ -1232,27 +1140,6 @@ such as reverse proxies and load balancers.")
     (description "Minimalistic StatsD client for Node.js programs.")
     (license license:expat)))
 
-(define-public node-mersenne
-  (package
-    (name "node-mersenne")
-    (version "0.0.4")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/jwatte/node-mersenne")
-               (commit "f9fa01694ee49d6ae6ff9d90cfda594bddd3ccef"))) ; release is untagged
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "034iaiq2pdqn342p2404cpz364g282d2hkp9375hysnh9i968wbb"))))
-    (build-system node-build-system)
-    (arguments '(#:tests? #f)) ; No tests.
-    (home-page "http://www.enchantedage.com/node-mersenne")
-    (synopsis "node.js module for generating Mersenne Twister random numbers")
-    (description "Node.js port of the Mersenne Twister random number generator.")
-    (license license:bsd-3)))
-
 (define-public node-ms
   (package
     (name "node-ms")
@@ -1315,29 +1202,6 @@ such as reverse proxies and load balancers.")
     (description "Run the supplied function exactly one time (once).")
     (license license:expat)))
 
-(define-public node-oop
-  (let ((commit "f9d87cda0958886955c14a0a716e57021ed295dc")
-        (revision "1"))
-    (package
-      (name "node-oop")
-      (version (git-version "0.0.0" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                 (url "https://github.com/felixge/node-oop")
-                 (commit commit)))
-          (file-name (git-file-name name version))
-          (sha256
-           (base32
-            "0mqrcf0xi2jbwffwkk00cljpqfsri1jk8s6kz8jny45apn7zjds1"))))
-      (build-system node-build-system)
-      (arguments '(#:tests? #f)) ; Tests run during build phase.
-      (home-page "https://github.com/felixge/node-oop")
-      (synopsis "Simple & light-weight oop")
-      (description "This library tries to bring basic oop features to JavaScript while being as light-weight and simple as possible.")
-      (license license:expat))))
-
 (define-public node-process-nextick-args
   (package
     (name "node-process-nextick-args")
@@ -1526,56 +1390,6 @@ Google Maps, and others.")
     (description "Simply swizzle your arguments.")
     (license license:expat)))
 
-(define-public node-stack-trace
-  (package
-    (name "node-stack-trace")
-    (version "0.0.10")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/felixge/node-stack-trace")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "1vci7qmkmrhgvncz24ihwpi7ivwj6ffw63l0jd216lgmlcv3xscg"))))
-    (build-system node-build-system)
-    (arguments
-     '(#:tests? #f
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'build)) ; 'make' runs the test suite.
-       ))
-    (native-inputs
-     `(("node-far" ,node-far)
-       ("node-long-stack-traces" ,node-long-stack-traces)))
-    (home-page "https://github.com/felixge/node-stack-trace")
-    (synopsis "Get v8 stack traces as an array of CallSite objects")
-    (description "Get v8 stack traces as an array of CallSite objects.")
-    (license license:expat)))
-
-(define-public node-statsd-parser
-  (package
-    (name "node-statsd-parser")
-    (version "0.0.4")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/dscape/statsd-parser")
-               (commit version)))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "049rnczsd6pv6bk282q4w72bhqc5cs562djgr7yncy7lk0wzq5j3"))))
-    (build-system node-build-system)
-    (arguments '(#:tests? #f)) ; No tests.
-    (home-page "https://github.com/dscape/statsd-parser")
-    (synopsis "Streaming parser for the statsd protocol")
-    (description "Streaming parser for the statsd protocol used in node-lynx.")
-    (license license:asl2.0)))
-
 (define-public node-storage-engine
   (package
     (name "node-storage-engine")
@@ -1728,27 +1542,6 @@ from C are supported as well as some other extensions from Ruby.")
     (description "Definitions of levels for logging purposes & shareable Symbol constants.")
     (license license:expat)))
 
-(define-public node-util-deprecate
-  (package
-    (name "node-util-deprecate")
-    (version "1.0.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/TooTallNate/util-deprecate")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "0npj4mksv10z6l0q1m84s263xx4afrmgq6f2v7y29gam2phifz6n"))))
-    (build-system node-build-system)
-    (arguments '(#:tests? #f)) ; No test suite.
-    (home-page "https://github.com/TooTallNate/util-deprecate")
-    (synopsis "The Node.js `util.deprecate()` function with browser support")
-    (description "The Node.js `util.deprecate()` function with browser support.")
-    (license license:expat)))
-
 (define-public node-winston
   (package
     (name "node-winston")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 109c9f7..b69dd91 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -24,9 +24,10 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
-  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages statistics)
@@ -38,7 +39,6 @@
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
-  #:use-module (gnu packages python-xyz)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm
index 7aa706c..d9b5694 100644
--- a/gn/packages/python24.scm
+++ b/gn/packages/python24.scm
@@ -109,10 +109,63 @@ read read ssl ssl tcl tcl tk tk ,(version-major+minor (package-version tcl)) ,(v
         (let ((python (resolve-interface '(gn packages python24))))
               (module-ref python 'python-2.4)))
 
+;; We borrow this from (guix build-system python) since we cannot refer to it
+;; with the magic '@@' symbol since Guix has switched to guile-3.0.
+(define* (package-with-explicit-python python old-prefix new-prefix
+                                       #:key variant-property)
+  "Return a procedure of one argument, P.  The procedure creates a package with
+the same fields as P, which is assumed to use PYTHON-BUILD-SYSTEM, such that
+it is compiled with PYTHON instead.  The inputs are changed recursively
+accordingly.  If the name of P starts with OLD-PREFIX, this is replaced by
+NEW-PREFIX; otherwise, NEW-PREFIX is prepended to the name.
+
+When VARIANT-PROPERTY is present, it is used as a key to search for
+pre-defined variants of this transformation recorded in the 'properties' field
+of packages.  The property value must be the promise of a package.  This is a
+convenient way for package writers to force the transformation to use
+pre-defined variants."
+  (define package-variant
+    (if variant-property
+        (lambda (package)
+          (assq-ref (package-properties package)
+                    variant-property))
+        (const #f)))
+
+  (define (transform p)
+    (cond
+     ;; If VARIANT-PROPERTY is present, use that.
+     ((package-variant p)
+      => force)
+
+     ;; Otherwise build the new package object graph.
+     ((eq? (package-build-system p) python-build-system)
+      (package
+        (inherit p)
+        (location (package-location p))
+        (name (let ((name (package-name p)))
+                (string-append new-prefix
+                               (if (string-prefix? old-prefix name)
+                                   (substring name
+                                              (string-length old-prefix))
+                                   name))))
+        (arguments
+         (let ((python (if (promise? python)
+                           (force python)
+                           python)))
+           (ensure-keyword-arguments (package-arguments p)
+                                     `(#:python ,python))))))
+     (else p)))
+
+  (define (cut? p)
+    (or (not (eq? (package-build-system p) python-build-system))
+        (package-variant p)))
+
+  (package-mapping transform cut?))
+
 (define package-with-python24
-  ((@@ (guix build-system python) package-with-explicit-python) (delay (default-python2.4))
-                                                                "python-" "python24-"
-                                                                #:variant-property 'python24-variant))
+  (package-with-explicit-python (delay (default-python2.4))
+                                "python-" "python24-"
+                                #:variant-property 'python24-variant))
 
 (define (strip-python24-variant p)
   (package