Add (pangenomes) gfalook

2 files changed, 166 insertions, 1 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index cff50d5..fffd077 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -2362,6 +2362,67 @@
   (crate-source "zlib-rs" "0.6.3"
                 "04qmv85amq6sv73bzqgvnlsk9mnrl97rygzf2v4zjcx1807d9qrv"))
 
+;; gfalook-specific crates
+(define rust-bitflags-2.11.1
+  (crate-source "bitflags" "2.11.1"
+                "1cvqijg3rvwgis20a66vfdxannjsxfy5fgjqkaq3l13gyfcj4lf4"))
+
+(define rust-byteorder-lite-0.1.0
+  (crate-source "byteorder-lite" "0.1.0"
+                "15alafmz4b9az56z6x7glcbcb6a8bfgyd109qc3bvx07zx4fj7wg"))
+
+(define rust-clap-4.6.1
+  (crate-source "clap" "4.6.1"
+                "0lcf88l7vlg796rrqr7wipbbmfa5sgsgx4211b7xmxxv8dz13nqx"))
+
+(define rust-clap-derive-4.6.1
+  (crate-source "clap_derive" "4.6.1"
+                "1acpz49hi00iv9jkapixjzcv7s51x8qkfaqscjm36rqgf428dkpj"))
+
+(define rust-fdeflate-0.3.7
+  (crate-source "fdeflate" "0.3.7"
+                "130ga18vyxbb5idbgi07njymdaavvk6j08yh1dfarm294ssm6s0y"))
+
+(define rust-image-0.25.10
+  (crate-source "image" "0.25.10"
+                "0131b9fsd5grxf3lchfs2ci0rg8ga2mh1ygai7k2zh1k8cwq1aw5"))
+
+(define rust-jiff-0.2.23
+  (crate-source "jiff" "0.2.23"
+                "0nc37n7jvgrzxdkcgc2hsfdf70lfagigjalh4igjrm5njvf4cd8s"))
+
+(define rust-jiff-static-0.2.23
+  (crate-source "jiff-static" "0.2.23"
+                "192ss3cnixvg79cpa76clwkhn4mmz10vnwsbf7yjw8i484s8p31a"))
+
+(define rust-libc-0.2.185
+  (crate-source "libc" "0.2.185"
+                "13rbdaa59l3w92q7kfcxx8zbikm99zzw54h59aqvcv5wx47jrzsj"))
+
+(define rust-moxcms-0.8.1
+  (crate-source "moxcms" "0.8.1"
+                "0jz4fd5f7pdn1rngqc96lxriqjkym1lswdhdbjr037s8p9ac31dv"))
+
+(define rust-png-0.18.1
+  (crate-source "png" "0.18.1"
+                "0qca282xp8a6d7mikxrwji3f52mjn4vnqxz2v9iz5adj665rnxk0"))
+
+(define rust-portable-atomic-util-0.2.6
+  (crate-source "portable-atomic-util" "0.2.6"
+                "18wrsx7fjwc2kgbpfjfm3igv3vdzsidmjhbqivjln7d0c6z9f4q9"))
+
+(define rust-pxfm-0.1.28
+  (crate-source "pxfm" "0.1.28"
+                "17bbi6r9jiz9rmlj9zwjcf3qrivr33l8vwjmj9y812ysagkl385m"))
+
+(define rust-rayon-1.12.0
+  (crate-source "rayon" "1.12.0"
+                "0vcj63xgnk72c30vdrak7dhl53snnaqv9x2faf1d94hzg1kb2fgv"))
+
+(define rust-rustc-hash-2.1.2
+  (crate-source "rustc-hash" "2.1.2"
+                "1gjdc5bw9982cj176jvgz9rrqf9xvr1q1ddpzywf5qhs7yzhlc4l"))
+
 (define-cargo-inputs lookup-cargo-inputs
   (gfainject =>
     (list rust-adler-1.0.2
@@ -3382,7 +3443,75 @@
           rust-winapi-i686-pc-windows-gnu-0.4.0
           rust-winapi-x86-64-pc-windows-gnu-0.4.0
           rust-wyhash-0.5.0
-          rust-zlib-rs-0.6.3)))
+          rust-zlib-rs-0.6.3))
+  (gfalook =>
+    (list rust-adler2-2.0.1
+          rust-aho-corasick-1.1.4
+          rust-anstream-1.0.0
+          rust-anstyle-1.0.14
+          rust-anstyle-parse-1.0.0
+          rust-anstyle-query-1.1.5
+          rust-anstyle-wincon-3.0.11
+          rust-autocfg-1.5.0
+          rust-bitflags-2.11.1
+          rust-block-buffer-0.10.4
+          rust-bytemuck-1.25.0
+          rust-byteorder-lite-0.1.0
+          rust-cfg-if-1.0.4
+          rust-clap-4.6.1
+          rust-clap-builder-4.6.0
+          rust-clap-derive-4.6.1
+          rust-clap-lex-1.1.0
+          rust-colorchoice-1.0.5
+          rust-cpufeatures-0.2.17
+          rust-crc32fast-1.5.0
+          rust-crossbeam-deque-0.8.6
+          rust-crossbeam-epoch-0.9.18
+          rust-crossbeam-utils-0.8.21
+          rust-crypto-common-0.1.7
+          rust-digest-0.10.7
+          rust-either-1.15.0
+          rust-env-filter-1.0.1
+          rust-env-logger-0.11.10
+          rust-fdeflate-0.3.7
+          rust-flate2-1.1.9
+          rust-generic-array-0.14.7
+          rust-heck-0.5.0
+          rust-image-0.25.10
+          rust-is-terminal-polyfill-1.70.2
+          rust-jiff-0.2.23
+          rust-jiff-static-0.2.23
+          rust-libc-0.2.185
+          rust-log-0.4.29
+          rust-memchr-2.8.0
+          rust-miniz-oxide-0.8.9
+          rust-moxcms-0.8.1
+          rust-num-traits-0.2.19
+          rust-once-cell-polyfill-1.70.2
+          rust-png-0.18.1
+          rust-portable-atomic-1.13.1
+          rust-portable-atomic-util-0.2.6
+          rust-proc-macro2-1.0.106
+          rust-pxfm-0.1.28
+          rust-quote-1.0.45
+          rust-rayon-1.12.0
+          rust-rayon-core-1.13.0
+          rust-regex-1.12.3
+          rust-regex-automata-0.4.14
+          rust-regex-syntax-0.8.10
+          rust-rustc-hash-2.1.2
+          rust-serde-core-1.0.228
+          rust-serde-derive-1.0.228
+          rust-sha2-0.10.9
+          rust-simd-adler32-0.3.9
+          rust-strsim-0.11.1
+          rust-syn-2.0.117
+          rust-typenum-1.19.0
+          rust-unicode-ident-1.0.24
+          rust-utf8parse-0.2.2
+          rust-version-check-0.9.5
+          rust-windows-link-0.2.1
+          rust-windows-sys-0.61.2)))
 
 ;;;
 ;;; Main package.
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 1761e98..4d99cf5 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -1234,6 +1234,41 @@ supporting pangenomic applications following the PanSN hierarchical naming
 specification.")
     (license license:expat))))
 
+(define-public gfalook
+  (let ((commit "5199d77ecc4980b181177c16b94f6e56c0d06e4c")
+        (revision "1"))
+    (package
+      (name "gfalook")
+      (version (git-version "0.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/pangenome/gfalook")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "0138abzw0x2fy94k09vi740am8haby2030mi03cl0gzjnf39q5cq"))))
+      (build-system cargo-build-system)
+      (arguments
+       (list #:install-source? #f
+             #:tests? #f
+             #:phases
+             #~(modify-phases %standard-phases
+                 (add-after 'unpack 'reduce-image-features
+                   (lambda _
+                     ;; Only PNG output is used; disable other image formats to
+                     ;; reduce heavy transitive dependency tree.
+                     (substitute* "Cargo.toml"
+                       (("image = \"0\\.25\"")
+                        "image = { version = \"0.25\", default-features = false, features = [\"png\"] }")))))))
+      (inputs (cargo-inputs 'gfalook
+                            #:module '(gn packages pangenome-rust)))
+      (home-page "https://github.com/pangenome/gfalook")
+      (synopsis "GFA visualization tool")
+      (description "gfalook is a Rust reimplementation of odgi viz,
+producing PNG and SVG visualizations of pangenome graphs in GFA format.")
+      (license license:expat))))
+
 (define-public pafplot
   (let ((commit "2785b0ef30d37300afc77fd4b04d1d949c143551")
         (revision "1"))
@@ -1282,6 +1317,7 @@ between sequences.")
            gafpack
            gfaffix
            gfainject
+           gfalook
            gfautil
            htslib
            impg