Downgrade to wfmash-0.14 for mempang and add tools for the workshop

2 files changed, 5 insertions, 2 deletions

diff --git a/README.org b/README.org
index 94e9525..55439d4 100644
--- a/README.org
+++ b/README.org
@@ -23,7 +23,7 @@ To easily use the packages from this repo, simply add it to your `channels` list
 and run /guix pull/ like normal to update your software. E.g.
 
 #+BEGIN_SRC sh
-  guix pull --url=https://codeberg.org/guix/guix -p ~/opt/guix-pull  --channels=channels.scm
+  guix pull --url=https://codeberg.org/guix/guix -p ~/opt/guix-bioinformatics  --channels=channels.scm
 #+END_SRC
 
 The channel file actually accesses https://git.genenetwork.org/guix-bioinformatics/tree/.guix-channel which pulls other channels and fixates the hashes. The commit hash b0fa1dc can be found from the guix you want to run with /guix -V/, it speeds up installation and makes it reproducible. Note that the upstream channel may override that version.
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index b82845e..ad7e37b 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -1509,7 +1509,7 @@ between sequences.")
            vcflib
            vg
            wally
-           wfmash))
+           wfmash-0.14))
     (home-page "https://github.com/pangenome")
     (synopsis "Pangenome tools collection")
     (description "Meta package that provides the main pangenome tools:
@@ -1534,9 +1534,11 @@ kfilt, miniprot, pangene, wally, and vcfbub.")
      (list pangenomes
            bc
            bcftools
+           coreutils
            fastix
            gnuplot
            graphviz
+           grep
            gzip
            multiqc
            mummer
@@ -1548,6 +1550,7 @@ kfilt, miniprot, pangene, wally, and vcfbub.")
            python-pycairo
            rtg-tools
            r-minimal
+           sed
            r-ape
            r-data-table
            r-gggenes