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

1 files changed, 90 insertions, 1 deletions

diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 3051dcb..553fbd7 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -7,6 +7,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
@@ -20,6 +21,9 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages cran)
+  #:use-module (gn packages crates-io)
+  #:use-module (gnu packages crates-io)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages cpio)
   #:use-module (gn packages elixir)
@@ -53,6 +57,7 @@
   #:use-module (gn packages javascript)
   #:use-module (gn packages phewas)
   #:use-module (gn packages python)
+  #:use-module (gn packages python24)
   #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
@@ -167,6 +172,41 @@ bootstrap resampling to estimate the confidence region for the
 location of a putative QTL.")
     (license license:gpl2+))))
 
+(define-public python24-qtlreaper
+  (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
+  (package
+    (name "python24-qtlreaper")
+    (version (string-append "1.1-gn2-" (string-take commit 7) ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   ;; (url "https://github.com/genenetwork/genenetwork2.git")
+                   (url "https://github.com/pjotrp/QTLreaper.git")
+                   (commit commit)))
+             (file-name (string-append name "-" (string-take commit 7)))
+             (sha256
+              (base32
+               "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2.4
+       #:tests? #f))   ; no 'setup.py test' really!
+    (native-inputs
+     `(("python24-setuptools" ,python24-setuptools)))
+    (home-page "http://qtlreaper.sourceforge.net/")
+    (synopsis "Scan expression data for QTLs")
+    (description
+     "Batch-oriented version of WebQTL. It requires, as input,
+expression data from members of a set of recombinant inbred lines and
+genotype information for the same lines.  It searches for an
+association between each expression trait and all genotypes and
+evaluates that association by a permutation test.  For the permutation
+test, it performs only as many permutations as are necessary to define
+the empirical P-value to a reasonable precision. It also performs
+bootstrap resampling to estimate the confidence region for the
+location of a putative QTL.")
+    (license license:gpl2+))))
+
 (define-public python-qtlreaper
   (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
   (package
@@ -207,6 +247,55 @@ bootstrap resampling to estimate the confidence region for the
 location of a putative QTL.")
     (license license:gpl2+))))
 
+(define-public rust-qtlreaper
+  (let ((commit "eacf6ff1c3d1cd16084a70a7a425bd77080c15de")
+        (revision "1"))
+    (package
+      (name "rust-qtlreaper")
+      (version (git-version "0.1.3" revision commit))
+      (source
+        (origin
+          (method git-fetch)
+          (uri (git-reference
+                 (url "https://github.com/chfi/rust-qtlreaper.git")
+                 (commit commit)))
+          (file-name (git-file-name name version))
+          (sha256
+           (base32
+            "0gr2z54i11zz94ra4w06fhfnwnmmhl5xyc8qhlk0v2qq18yfi7ji"))))
+      (build-system cargo-build-system)
+      (arguments
+       `(#:cargo-inputs
+         (("rust-rand" ,rust-rand-0.6)
+          ("rust-structopt" ,rust-structopt)
+          ("rust-rayon" ,rust-rayon-1.0)
+          ("rust-serde" ,rust-serde)
+          ("rust-serde-json" ,rust-serde-json))
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'configure 'regenerate-cargo-lock
+             (lambda _
+               (delete-file "Cargo.lock")
+               (invoke "cargo" "generate-lockfile")))
+           (add-after 'patch-generated-file-shebangs 'patch-cargo-checksums
+             (lambda _
+               (use-modules (guix build cargo-utils))
+                 (for-each
+                   (lambda (filename)
+                     (use-modules (guix build cargo-utils))
+                     (delete-file filename)
+                     (let* ((dir (dirname filename)))
+                       (display (string-append
+                                  "patch-cargo-checksums: generate-checksums for "
+                                  dir "\n"))
+                       (generate-checksums dir)))
+                   (find-files "guix-vendor" ".cargo-checksum.json"))
+                 #t)))))
+      (home-page "https://github.com/chfi/rust-qtlreaper")
+      (synopsis "Reimplementation of genenetwork/QTLReaper in Rust")
+      (description "Reimplementation of genenetwork/QTLReaper in Rust")
+      (license #f))))
+
 (define-public genenetwork2
   (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
   (package
@@ -247,7 +336,7 @@ location of a putative QTL.")
 	      ("python2-pillow" ,python2-pillow)
               ("python2-cssselect" ,python2-cssselect)
               ("python2-elasticsearch" ,python2-elasticsearch)
-              ("python2-htmlgen-gn" ,python2-htmlgen-gn)
+              ("python2-htmlgen" ,python2-htmlgen)
               ("python2-jinja2" ,python2-jinja2)
               ("python2-sqlalchemy" ,python2-sqlalchemy)
               ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)