Add manifest.scm to build all critical packages

2 files changed, 45 insertions, 1 deletions

diff --git a/README.org b/README.org
index a343b94..6e63108 100644
--- a/README.org
+++ b/README.org
@@ -3,7 +3,9 @@
 IMPORTANT: this repository lives at https://git.genenetwork.org/guix-bioinformatics/!
 Older packages have been moved to https://git.genenetwork.org/guix-bioinformatics-past/.
 
-Bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places.
+Over 400 bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places.
+Mostly targetting genomics, pangenomics and genetics.
+
 See Guix documentation and [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for installing and hacking Guix.
 
 See [[https://github.com/franzos/awesome-guix][awesome guix]] for a list of other channels.
@@ -67,6 +69,12 @@ root with
 : guix archive --authorize < tux02-guix-substitutions-public-key.txt
 : guix build -L ~/guix-bioinformatics/ --substitute-urls="https://cuirass.genenetwork.org https://ci.guix.gnu.org https://bordeaux.guix.gnu.org https://guix.genenetwork.org" hello
 
+* Testing the build
+
+All important packages are listed in manifest.scm. Test with
+
+: guix build -L . -m manifest.scm
+
 * An important note on AI
 
 The packages in guix-bioinformatics channel are generally written with the help of AI. Only the directory ./gnu/packages contains software that was crafted by hand without the help of AI.
diff --git a/manifest.scm b/manifest.scm
new file mode 100644
index 0000000..a7140bd
--- /dev/null
+++ b/manifest.scm
@@ -0,0 +1,36 @@
+;; Guix manifest for all end-node packages in guix-bioinformatics.
+;; These are packages not depended on by other packages in this channel.
+;;
+;; Usage:
+;;   guix build -L guix-bioinformatics -m manifest.scm
+;;
+
+(specifications->manifest
+ '(
+   "bnw"
+   "bwa-mem2"
+   "cosigt"
+   "gafpack"
+   "gemma-wrapper"
+   "genenetwork2"
+   "genenetwork3"
+   "gfainject"
+   "gfautil"
+   "gn-auth"
+   "gn-guile"
+   "gn-libs"
+   "gn-proxy"
+   "gn-uploader"
+   "impg"
+   "julia-pluto"
+   "logtodo"
+   "mbg"
+   "meryl"
+   "miniprot"
+   "moosefs"
+   "odgi"
+   "pangene"
+   "pggb"
+   "seqwish"
+   "smoothxg"
+   ))