Move (gfaffix) to rust package

2 files changed, 214 insertions, 25 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a50a44d..83dd2b8 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -635,31 +635,6 @@ integration with gPLINK and Haploview, there is some support for the
 subsequent visualization, annotation and storage of results.")
     (license license:gpl3+))))
 
-(define-public gfaffix
-  (package
-    (name "gfaffix")
-    (version "0.2.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/marschall-lab/GFAffix")
-               (commit version)))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0yn8i70ww3x544qm4fwr33vklsxf3fvivpfpv46prkfz9hsmd9ps"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:install-source? #f))
-    (inputs (cargo-inputs 'gfaffix
-                          #:module '(gn packages rust-crates)))
-    (home-page "https://github.com/marschall-lab/GFAffix")
-    (synopsis "Identify walk-preserving shared affixes in variation graphs")
-    (description
-     "GFAffix identifies walk-preserving shared affixes in variation graphs and
-collapses them into a non-redundant graph structure.")
-    (license license:expat)))
-
 (define-public graphaligner
   (package
     (name "graphaligner")
diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index 41092bf..1399f24 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -2096,6 +2096,93 @@
   (crate-source "unicode-width" "0.1.14"
                 "1bzn2zv0gp8xxbxbhifw778a7fc93pa6a1kj24jgg9msj07f7mkx"))
 
+;;; Crate sources for gfaffix
+
+(define rust-anyhow-1.0.101
+  (crate-source "anyhow" "1.0.101"
+                "1skmg90fnjnlgs3vl7bksw7036d3rqwqj20n2fxd2ppg67p0y3jz"))
+
+(define rust-clap-4.5.59
+  (crate-source "clap" "4.5.59"
+                "16b4kgj909yyshz9kj7nkalbyi46yz1lrhqha54wbbn32x6zgjn5"))
+
+(define rust-clap-builder-4.5.59
+  (crate-source "clap_builder" "4.5.59"
+                "094fc76nsq3v52r1a9rbwix22cqnda8p2wr2a24j302v0r2sl39p"))
+
+(define rust-jiff-0.2.20
+  (crate-source "jiff" "0.2.20"
+                "0hv59kcqj5sc0jgk4q7yrq5dp8yb3qlan98qk3s36sq9ribc6ry8"))
+
+(define rust-jiff-static-0.2.20
+  (crate-source "jiff-static" "0.2.20"
+                "1rcvbp9aj8ll4ljxcgzq4l2h9idmkb0v6mdvf3r3i5r64m1np57p"))
+
+(define rust-regex-syntax-0.8.9
+  (crate-source "regex-syntax" "0.8.9"
+                "0k0a47r1rcl794wj8a948niakbg081s5pp5nlgcbmmr2iy3qfs59"))
+
+(define rust-rustix-1.1.3
+  (crate-source "rustix" "1.1.3"
+                "0d0z2zcw4rwzni1hm8snw8xdxwwrij336m31c4ghq66cghj9wv0l"))
+
+(define rust-syn-2.0.116
+  (crate-source "syn" "2.0.116"
+                "1jv9pk48qmhn6yrdfl3lngy5i74wg7gcx13gfhvm4s8q0p3j9x1x"))
+
+(define rust-terminal-size-0.4.3
+  (crate-source "terminal_size" "0.4.3"
+                "1l7cicmz49c0cyskfp5a389rsai649xi7y032v73475ikjbwpf30"))
+
+(define rust-windows-aarch64-gnullvm-0.53.1
+  (crate-source "windows_aarch64_gnullvm" "0.53.1"
+                "0lqvdm510mka9w26vmga7hbkmrw9glzc90l4gya5qbxlm1pl3n59"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-windows-aarch64-msvc-0.53.1
+  (crate-source "windows_aarch64_msvc" "0.53.1"
+                "01jh2adlwx043rji888b22whx4bm8alrk3khjpik5xn20kl85mxr"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-windows-i686-gnu-0.53.1
+  (crate-source "windows_i686_gnu" "0.53.1"
+                "18wkcm82ldyg4figcsidzwbg1pqd49jpm98crfz0j7nqd6h6s3ln"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-windows-i686-gnullvm-0.53.1
+  (crate-source "windows_i686_gnullvm" "0.53.1"
+                "030qaxqc4salz6l4immfb6sykc6gmhyir9wzn2w8mxj8038mjwzs"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-windows-i686-msvc-0.53.1
+  (crate-source "windows_i686_msvc" "0.53.1"
+                "1hi6scw3mn2pbdl30ji5i4y8vvspb9b66l98kkz350pig58wfyhy"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-windows-targets-0.53.5
+  (crate-source "windows-targets" "0.53.5"
+                "1wv9j2gv3l6wj3gkw5j1kr6ymb5q6dfc42yvydjhv3mqa7szjia9"))
+
+(define rust-windows-x86-64-gnu-0.53.1
+  (crate-source "windows_x86_64_gnu" "0.53.1"
+                "16d4yiysmfdlsrghndr97y57gh3kljkwhfdbcs05m1jasz6l4f4w"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-windows-x86-64-gnullvm-0.53.1
+  (crate-source "windows_x86_64_gnullvm" "0.53.1"
+                "1qbspgv4g3q0vygkg8rnql5c6z3caqv38japiynyivh75ng1gyhg"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-windows-x86-64-msvc-0.53.1
+  (crate-source "windows_x86_64_msvc" "0.53.1"
+                "0l6npq76vlq4ksn4bwsncpr8508mk0gmznm6wnhjg95d19gzzfyn"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-libz-sys-1.1.23
+  ;; TODO: Check bundled sources.
+  (crate-source "libz-sys" "1.1.23"
+                "1xy0l46gmhfyk28r9pm7njl0h7dh8l2vpiqw67kn043pyfxiil8m"))
+
 (define-cargo-inputs lookup-cargo-inputs
   (gfainject =>
     (list rust-adler-1.0.2
@@ -2768,6 +2855,108 @@
           rust-wit-bindgen-rust-macro-0.51.0
           rust-wit-component-0.244.0
           rust-wit-parser-0.244.0))
+  (gfaffix =>
+    (list rust-adler2-2.0.1
+          rust-aho-corasick-1.1.4
+          rust-anstream-0.6.21
+          rust-anstyle-1.0.13
+          rust-anstyle-parse-0.2.7
+          rust-anstyle-query-1.1.5
+          rust-anstyle-wincon-3.0.11
+          rust-anyhow-1.0.101
+          rust-arrayvec-0.5.2
+          rust-autocfg-1.5.0
+          rust-bitflags-1.3.2
+          rust-bitflags-2.11.0
+          rust-boomphf-0.5.9
+          rust-bstr-0.2.17
+          rust-bytemuck-1.25.0
+          rust-bytemuck-derive-1.10.2
+          rust-byteorder-1.5.0
+          rust-cc-1.2.56
+          rust-cfg-if-1.0.4
+          rust-clap-4.5.59
+          rust-clap-builder-4.5.59
+          rust-clap-derive-4.5.55
+          rust-clap-lex-1.0.0
+          rust-colorchoice-1.0.4
+          rust-crc32fast-1.5.0
+          rust-crossbeam-channel-0.5.15
+          rust-crossbeam-deque-0.8.6
+          rust-crossbeam-epoch-0.9.18
+          rust-crossbeam-utils-0.8.21
+          rust-either-1.15.0
+          rust-env-filter-1.0.0
+          rust-env-logger-0.11.9
+          rust-equivalent-1.0.2
+          rust-errno-0.3.14
+          rust-find-msvc-tools-0.1.9
+          rust-flate2-1.1.9
+          rust-fnv-1.0.7
+          rust-gfa-0.10.1
+          rust-handlegraph-0.7.0-alpha.9
+          rust-hashbrown-0.16.1
+          rust-heck-0.5.0
+          rust-indexmap-2.13.0
+          rust-is-terminal-polyfill-1.70.2
+          rust-jiff-0.2.20
+          rust-jiff-static-0.2.20
+          rust-lazy-static-1.5.0
+          rust-lexical-core-0.7.6
+          rust-libc-0.2.182
+          rust-libz-sys-1.1.23
+          rust-linux-raw-sys-0.11.0
+          rust-log-0.4.29
+          rust-memchr-2.8.0
+          rust-memmap-0.7.0
+          rust-miniz-oxide-0.8.9
+          rust-nom-5.1.3
+          rust-num-traits-0.2.19
+          rust-once-cell-polyfill-1.70.2
+          rust-pkg-config-0.3.32
+          rust-portable-atomic-1.13.1
+          rust-portable-atomic-util-0.2.5
+          rust-proc-macro2-1.0.106
+          rust-quote-1.0.44
+          rust-rand-core-0.6.4
+          rust-rayon-1.11.0
+          rust-rayon-core-1.13.0
+          rust-regex-1.12.3
+          rust-regex-automata-0.1.10
+          rust-regex-automata-0.4.14
+          rust-regex-syntax-0.8.9
+          rust-rustc-hash-2.1.1
+          rust-rustix-1.1.3
+          rust-ryu-1.0.23
+          rust-serde-core-1.0.228
+          rust-serde-derive-1.0.228
+          rust-shlex-1.3.0
+          rust-simd-adler32-0.3.8
+          rust-static-assertions-1.1.0
+          rust-strsim-0.11.1
+          rust-succinct-0.5.2
+          rust-syn-2.0.116
+          rust-terminal-size-0.4.3
+          rust-unicode-ident-1.0.24
+          rust-utf8parse-0.2.2
+          rust-vcpkg-0.2.15
+          rust-version-check-0.9.5
+          rust-winapi-0.3.9
+          rust-winapi-i686-pc-windows-gnu-0.4.0
+          rust-winapi-x86-64-pc-windows-gnu-0.4.0
+          rust-windows-link-0.2.1
+          rust-windows-sys-0.60.2
+          rust-windows-sys-0.61.2
+          rust-windows-targets-0.53.5
+          rust-windows-aarch64-gnullvm-0.53.1
+          rust-windows-aarch64-msvc-0.53.1
+          rust-windows-i686-gnu-0.53.1
+          rust-windows-i686-gnullvm-0.53.1
+          rust-windows-i686-msvc-0.53.1
+          rust-windows-x86-64-gnu-0.53.1
+          rust-windows-x86-64-gnullvm-0.53.1
+          rust-windows-x86-64-msvc-0.53.1
+          rust-wyhash-0.5.0))
   (gfautil =>
     (list rust-aho-corasick-1.1.4
           rust-android-system-properties-0.1.5
@@ -3373,3 +3562,28 @@ and alignments for analysis.  It can also compute graphs for the sequences.")
        "This package provides command line tools for working with @acronym{GFA,
 Graphical Fragment Assembly} files and related formats.")
       (license license:expat))))
+
+(define-public gfaffix
+  (package
+    (name "gfaffix")
+    (version "0.2.1")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/marschall-lab/GFAffix")
+               (commit version)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0yn8i70ww3x544qm4fwr33vklsxf3fvivpfpv46prkfz9hsmd9ps"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:install-source? #f))
+    (inputs (cargo-inputs 'gfaffix
+                          #:module '(gn packages pangenome-rust)))
+    (home-page "https://github.com/marschall-lab/GFAffix")
+    (synopsis "Identify walk-preserving shared affixes in variation graphs")
+    (description
+     "GFAffix identifies walk-preserving shared affixes in variation graphs and
+collapses them into a non-redundant graph structure.")
+    (license license:expat)))