From 6be47c5bc56b4a2d3183a58d1c9fb2e0846c7f0f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 11 Nov 2021 14:44:28 +0000
Subject: gnu: Add circtools.

* gnu/packages/bioinformatics.scm (circtools): New variable.
---
 gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ae3cf01c87..13bd7b5997 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -48,6 +48,7 @@
   #:use-module (guix hg-download)
   #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system go)
   #:use-module (guix build-system haskell)
@@ -77,6 +78,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages cran)
+  #:use-module (gnu packages crates-io)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages databases)
@@ -1390,6 +1392,61 @@ bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib
 compressed files.")
     (license license:expat)))
 
+(define-public circtools
+  (package
+    (name "circtools")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Kevinzjy/circtools")
+             ;; Corresponds to tag v1.0.0
+             (commit "79380de59013601021ca3b1352d6f64d2fb89646")
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0wg1s927g32k25j967kfr8l30nmr4c0p4zvy5igvy7cs6chd60lh"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))))
+         (add-after 'unpack 'prepare-spoa-dependencies
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "vendor/spoa/CMakeLists.txt"
+               (("find_package\\(bioparser 3.0.13 QUIET\\)")
+                "find_package(bioparser 3.0.13 CONFIG)")
+               (("find_package\\(biosoup 0.10.0 QUIET\\)")
+                "find_package(biosoup 0.10.0 CONFIG)")
+               (("GTest_FOUND") "TRUE")))))
+       #:cargo-inputs
+       (("rust-anyhow" ,rust-anyhow-1)
+        ("rust-bio" ,rust-bio-0.33)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-docopt" ,rust-docopt-1)
+        ("rust-flate2" ,rust-flate2-1)
+        ("rust-indicatif" ,rust-indicatif-0.15)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-seq-io" ,rust-seq-io-0.3))))
+    (inputs
+     `(("bioparser" ,bioparser)
+       ("biosoup" ,biosoup)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("pkg-config" ,pkg-config)
+       ("googletest" ,googletest)))
+    (home-page "https://github.com/Kevinzjy/circtools")
+    (synopsis "Accelerating functions in CIRI toolkit")
+    (description "This package provides accelerated functions for the CIRI
+toolkit.  It also provides the @code{ccs} executable to scan for circular
+consensus sequences.")
+    (license license:expat)))
+
 (define-public ciri-long
   (package
     (name "ciri-long")
-- 
cgit v1.2.3