Added (pangenome) pafplot

2 files changed, 101 insertions, 1 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index c4bdce9..cff50d5 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -2332,6 +2332,36 @@
 (define rust-vcf-0.6.1
   (crate-source "vcf" "0.6.1"
                 "0dc0p00a19rpmhrqcshrn2qg5l716b5s1fy8vpd3p32bw77vpbs0"))
+
+;; pafplot-specific crates
+(define rust-boomphf-0.6.0
+  (crate-source "boomphf" "0.6.0"
+                "0fzccz20w42lq2yfga4jdbgyhcjpjv1pl8xrvn1hb84052ajszk1"))
+
+(define rust-base64-0.21.7
+  (crate-source "base64" "0.21.7"
+                "0rw52yvsk75kar9wgqfwgb414kvil1gn7mqkrhn9zf1537mpsacx"))
+
+(define rust-line-drawing-1.0.1
+  (crate-source "line_drawing" "1.0.1"
+                "1a4fb7hbafqcys2lzyz87bqqnrsfiid3s8kgghab15kzdw0hkwxm"))
+
+(define rust-lodepng-3.12.2
+  (crate-source "lodepng" "3.12.2"
+                "1ni2dgxw3kzgwaywcvm43zviigk5rkflshhv781dqkh527dq4ygy"))
+
+(define rust-itertools-0.14.0
+  (crate-source "itertools" "0.14.0"
+                "118j6l1vs2mx65dqhwyssbrxpawa90886m3mzafdvyip41w2q69b"))
+
+(define rust-rgb-0.8.53
+  (crate-source "rgb" "0.8.53"
+                "1i0c55whln68zs6f5qqrkbg1mzai0p3qk1mwkwzdgr9i3dw4pcs7"))
+
+(define rust-zlib-rs-0.6.3
+  (crate-source "zlib-rs" "0.6.3"
+                "04qmv85amq6sv73bzqgvnlsk9mnrl97rygzf2v4zjcx1807d9qrv"))
+
 (define-cargo-inputs lookup-cargo-inputs
   (gfainject =>
     (list rust-adler-1.0.2
@@ -3311,7 +3341,48 @@
           rust-strsim-0.11.1
           rust-utf8parse-0.2.2
           rust-windows-link-0.2.1
-          rust-windows-sys-0.61.2)))
+          rust-windows-sys-0.61.2))
+  (pafplot =>
+    (list rust-adler2-2.0.1
+          rust-ansi-term-0.12.1
+          rust-atty-0.2.14
+          rust-autocfg-1.5.0
+          rust-base64-0.21.7
+          rust-bitflags-1.3.2
+          rust-boomphf-0.6.0
+          rust-bytemuck-1.25.0
+          rust-cfg-if-1.0.4
+          rust-clap-2.34.0
+          rust-crc32fast-1.5.0
+          rust-crossbeam-deque-0.8.6
+          rust-crossbeam-epoch-0.9.18
+          rust-crossbeam-utils-0.8.21
+          rust-either-1.15.0
+          rust-flate2-1.1.9
+          rust-fnv-1.0.7
+          rust-hermit-abi-0.1.19
+          rust-itertools-0.14.0
+          rust-libc-0.2.184
+          rust-libm-0.2.16
+          rust-line-drawing-1.0.1
+          rust-lodepng-3.12.2
+          rust-log-0.4.29
+          rust-miniz-oxide-0.8.9
+          rust-num-traits-0.2.19
+          rust-rand-core-0.6.4
+          rust-rayon-1.11.0
+          rust-rayon-core-1.13.0
+          rust-rgb-0.8.53
+          rust-simd-adler32-0.3.9
+          rust-strsim-0.8.0
+          rust-textwrap-0.11.0
+          rust-unicode-width-0.1.14
+          rust-vec-map-0.8.2
+          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-wyhash-0.5.0
+          rust-zlib-rs-0.6.3)))
 
 ;;;
 ;;; Main package.
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 141294e..1761e98 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -1234,6 +1234,33 @@ supporting pangenomic applications following the PanSN hierarchical naming
 specification.")
     (license license:expat))))
 
+(define-public pafplot
+  (let ((commit "2785b0ef30d37300afc77fd4b04d1d949c143551")
+        (revision "1"))
+    (package
+      (name "pafplot")
+      (version (git-version "0.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/pafplot")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "0aisssmmss4jxgnv04qk5gbnzzbzvakkcdr03swps3f1x22rfqdn"))))
+      (build-system cargo-build-system)
+      (arguments
+       (list #:install-source? #f
+             #:tests? #f))
+      (inputs (cargo-inputs 'pafplot
+                            #:module '(gn packages pangenome-rust)))
+      (home-page "https://github.com/ekg/pafplot")
+      (synopsis "Base-level dotplots from PAF alignments")
+      (description "pafplot renders whole-genome alignments in PAF format as
+raster dotplot images, drawing lines for each match to visualize homology
+between sequences.")
+      (license license:expat))))
+
 (define-public pangenomes
   (package
     (name "pangenomes")
@@ -1263,6 +1290,7 @@ specification.")
            minimap2
            miniprot
            odgi
+           pafplot
            pangene
            pggb
            samtools
@@ -1301,6 +1329,7 @@ kfilt, miniprot, pangene, wally, and vcfbub.")
            gnuplot
            multiqc
            mummer
+           pafplot
            parallel
            pigz
            python