From c2415bfa014892a56be9b621089a0a2ffab234f7 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 19 Sep 2023 19:24:04 +0300
Subject: Add fastix

---
 gn/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
 gn/packages/crates-io.scm      | 25 +++++++++++++++++++++++++
 2 files changed, 51 insertions(+)

(limited to 'gn/packages')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 2b1d514..4b37c8f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -548,6 +548,32 @@ remove these, as they provide little information for many downstream
 applications, such as haplotype panels or other imputation references.")
     (license license:expat)))
 
+(define-public fastix
+  (package
+    (name "fastix")
+    (version "0.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "fastix" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32 "1mzk65mg8vx0hz39xis6zqdmq56abhmza656gn9pgmlsn151gpx2"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:install-source? #f
+       #:cargo-inputs
+       (("rust-clap" ,rust-clap-2))
+       #:cargo-development-inputs
+       (("rust-assert-cmd" ,rust-assert-cmd-0.12)
+        ("rust-predicates" ,rust-predicates-1))))
+    (home-page "https://github.com/ekg/fastix")
+    (synopsis "Prefix-renaming FASTA records")
+    (description "A command line tool to add prefixes to FASTA headers.  The
+idea is to support pangenomic applications, following the
+@url{https://github.com/pangenome/PanSN-spec, PanSN} hierarchical naming
+specification.")
+    (license license:expat)))
+
 (define-public gafpack
   (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6")     ; November 10, 2022
         (revision "1"))
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 79832bc..557c980 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -10,6 +10,31 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages python))
 
+(define-public rust-assert-cmd-0.12
+  (package
+    (name "rust-assert-cmd")
+    (version "0.12.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "assert-cmd" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1xfn2spazxk3ljj9q3250a24gndja9vwa0h0rnbccdrbd4ncyvwk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-doc-comment" ,rust-doc-comment-0.3)
+        ("rust-escargot" ,rust-escargot-0.5)
+        ("rust-predicates" ,rust-predicates-1)
+        ("rust-predicates-core" ,rust-predicates-core-1)
+        ("rust-predicates-tree" ,rust-predicates-tree-1)
+        ("rust-wait-timeout" ,rust-wait-timeout-0.2))))
+    (home-page "https://github.com/assert-rs/assert_cmd")
+    (synopsis "Test CLI Applications.")
+    (description "Test CLI Applications.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-bgzip-0.2
   (package
     (name "rust-bgzip")
-- 
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