New package (pangenomes) meta-package

The pangenomes meta package propagates:

  wfmash, pggb, odgi, seqwish, smoothxg, impg, gfainject, gafpack, cosigt, minimap2, samtools, bedtools, bwa-mem2,
  meryl, kfilt, miniprot, pangene, gfaffix, gfautil, vcfbub, wally, fastga-rs, htslib

2 files changed, 46 insertions, 1 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index 7bd2d6b..817fc65 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -3879,7 +3879,7 @@ maps useful in haplotype-based genotyping.")
                     (commit commit)))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1j91b4mba0gpghix0sn6m6a81722vzhpf5a2b03ysrqsrvfykk5z"))))
+               (base32 "0sk2ab22z6qa00j1w8a8f5kbb7q2xb10fhd32zy4lh351v3mqmyg"))))
     (build-system cargo-build-system)
     (arguments (list #:install-source? #f))
     (inputs (cargo-inputs 'vcfbub #:module '(gn packages pangenome-rust)))
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 032bb75..1a4d6af 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -11,6 +11,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system trivial)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages boost)
@@ -771,3 +772,47 @@ sequences using wfmash, seqwish, smoothxg, and gfaffix.")
      (modify-inputs (package-inputs wfmash)
        (prepend jemalloc)
        (delete "libdeflate")))))
+
+(define-public pangenomes
+  (package
+    (name "pangenomes")
+    (version "1.0")
+    (source #f)
+    (build-system trivial-build-system)
+    (arguments
+     (list #:modules '((guix build utils))
+           #:builder
+           #~(begin
+               (use-modules (guix build utils))
+               (mkdir-p (string-append #$output "/bin")))))
+    (propagated-inputs
+     (list bedtools
+           bwa-mem2
+           cosigt
+           fastga-rs
+           gafpack
+           gfaffix
+           gfainject
+           gfautil
+           htslib
+           impg
+           kfilt
+           meryl
+           minimap2
+           miniprot
+           odgi
+           pangene
+           pggb
+           samtools
+           seqwish
+           smoothxg
+           vcfbub
+           wally
+           wfmash))
+    (home-page "https://github.com/pangenome")
+    (synopsis "Pangenome tools collection")
+    (description "Meta package that provides the main pangenome tools:
+wfmash, seqwish, smoothxg, odgi, pggb, impg, gfainject, gafpack, cosigt,
+and supporting tools like minimap2, samtools, bedtools, bwa-mem2, meryl,
+kfilt, miniprot, pangene, wally, and vcfbub.")
+    (license license:expat)))