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

1 files changed, 12 insertions, 71 deletions

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")