Mempang25 workshop

1 files changed, 58 insertions, 0 deletions

diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 5073c75..40c43a9 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -52,6 +52,11 @@
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages zig)
+  #:use-module (gnu packages bioconductor)
+  #:use-module (gnu packages crates-io)
+  #:use-module (gnu packages cran)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages wget)
   #:use-module (gn packages pangenome-rust)
   #:use-module (gnu packages python-xyz))
 
@@ -1193,6 +1198,28 @@ graphs.  It extends the original Bandage with new features including support
 for GFA format, annotations, and improved rendering.")
     (license license:gpl3+)))
 
+(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
+     (list #:install-source? #f
+           #:tests? #f  ; test deps not available
+           #:cargo-inputs `(("rust-clap" ,rust-clap-2))))
+    (home-page "https://github.com/ekg/fastix")
+    (synopsis "Prefix-renaming FASTA records")
+    (description "A command line tool to add prefixes to FASTA headers,
+supporting pangenomic applications following the PanSN hierarchical naming
+specification.")
+    (license license:expat)))
+
 (define-public pangenomes
   (package
     (name "pangenomes")
@@ -1239,3 +1266,34 @@ 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)))
+
+(define-public mempang-workshop
+  (package
+    (name "mempang-workshop")
+    (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 pangenomes
+           fastix
+           python
+           r-minimal
+           r-ape
+           r-gggenes
+           r-ggplot2
+           r-ggtree
+           r-tidyverse
+           wget
+           zstd))
+    (home-page "https://github.com/pangenome")
+    (synopsis "MEMPANG pangenome workshop tools")
+    (description "Meta package for the MEMPANG pangenome workshop.  Includes
+all pangenome tools plus R with plotting packages (ggplot2, gggenes, ape,
+ggtree, tidyverse) and supporting utilities (wget, zstd).")
+    (license license:expat)))