Note on AI (README) added a directory ./gnu/packages that will contain software that aligns with Guix upstream policies. pjotrp-w-claude

2 files changed, 14 insertions, 69 deletions

diff --git a/README.org b/README.org
index be8db7c..32164bb 100644
--- a/README.org
+++ b/README.org
@@ -2,16 +2,16 @@
 
 IMPORTANT: this repository has moved to https://git.genenetwork.org/guix-bioinformatics/!
 
-Bioinformatics packages for GNU Guix that are used in
-https://genenetwork.org/ and some other places.  See [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for
-installing and hacking GNU Guix. Other channels of bioinformatics
+Bioinformatics packages for Guix that are used in
+https://genenetwork.org/ and some other places.  See Guix documentation and [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for
+installing and hacking Guix. Other channels of bioinformatics
 interest can be found at
 
 1. https://github.com/BIMSBbioinfo
 2. https://github.com/UMCUGenetics/guix-additions
 3. https://github.com/ekg/guix-genomics
 
-Also see [[http://git.genenetwork.org/pjotrp/guix-notes/src/branch/master/CHANNELS.org][Guix notes]] for a list of channels.
+See [[https://github.com/franzos/awesome-guix][awesome guix]] for a list of channels.
 
 To easily use the packages from this repo, simply add it to your
 `channels` list in ~/.config/guix/channels.scm as described
@@ -47,68 +47,7 @@ or using a checked out Guix repo with
 : env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl
 
 Some (or most) of these package definitions should make it upstream
-into the GNU Guix repository when tested and stable.
-
-* Slurm and munge
-
-Install slurm with
-
-#+BEGIN_SRC bash
-    guix pull
-    guix package -i slurm-llnl
-
-    ~/.guix-profile/sbin/slurmd -C -D
-      ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909
-#+END_SRC
-
-
-* Common Workflow Language (CWL)
-
-/Note that CWL moved into Guix master!/
-
-Install the common workflow language tool cwltool from this repo with
-
-#+BEGIN_SRC bash
-
-    guix pull
-    export PATH=$HOME/.config/guix/current/bin/guix:$PATH
-    ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix package -i cwl-runner -p ~/opt/CWL
-
-The following package will be installed:
-   cwl-runner 1.0
-
-The following derivations will be built:
-   /gnu/store/ld59374zr45rbqanh7ccfi2wa4d5x4yl-cwl-runner-1.0.drv
-   /gnu/store/86j15mxj5zp3k3sjimhqhb6zsj19azsf-python-schema-salad-7.0.20200811075006.drv
-   /gnu/store/0q2ls0is3253r4gx6hs7kmvlcz412lh1-schema-salad-7.0.20200811075006.tar.gz.drv
-   /gnu/store/myj1365ph687ynahjhg6zqslrmd6zpjq-cwltool-3.0.20201117141248.drv
-
-source ~/opt/CWL/etc/profile
-cwltool --version
-  /gnu/store/50mncjcgc8vmq5dfrh0pb82avbzy8c4r-cwltool-3.0.20201117141248/bin/.cwltool-real 3.0
-#+END_SRC
-
-To run CWL definitions you can install tools in a Guix environment (avoiding
-Docker). Say you need mafft in a workflow
-
-#+begin_src sh
-    ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix environment \
-       guix --ad-hoc cwl-runner mafft
-#+end_src
-
-in the new shell you should be able to find both CWL and MAFFT:
-
-#+begin_src sh
-ls $GUIX_ENVIRONMENT/bin/cwl*
-/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwl-runner
-/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwltool
-ls $GUIX_ENVIRONMENT/bin/mafft
-/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/mafft
-#+end_src
-
-The paths can be loaded into the shell with
-
-: source $GUIX_ENVIRONMENT/etc/profile
+into the Guix repository when tested and stable.
 
 * Module system
 
@@ -124,7 +63,7 @@ with
       DATE=2012-12-21
 #+END_SRC
 
-Note that GNU Guix supercedes module functionality!
+Note that Guix supercedes module functionality!
 
 * Development tips
 
@@ -151,9 +90,14 @@ We run our own substitution server. Add the key to your machine as
 root with
 
 : guix archive --authorize < tux02-guix-substitutions-public-key.txt
-: guix build -L ~/guix-bioinformatics/ -L ~/guix-past/modules/ genenetwork2 --substitute-urls="https://ci.guix.gnu.org https://bordeaux.guix.gnu.org https://guix.genenetwork.org" --dry-run
+: guix build -L ~/guix-rust-past-crates/modules/ -L ~/guix-bioinformatics/ -L ~/guix-past/modules/  --substitute-urls="https://cuirass.genenetwork.org https://ci.guix.gnu.org https://bordeaux.guix.gnu.org https://guix.genenetwork.org" hello
+
+* 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.
+The packages in this directory align with Guix policy and may be upstreamed to guix trunk.
 
 * LICENSE
 
 These package descriptions (so-called Guix expressions) are
-distributed by the same license as GNU Guix, i.e. GPL3+
+distributed by the same license as Guix, i.e. GPL3+
diff --git a/gnu/packages/README_NO_AI.md b/gnu/packages/README_NO_AI.md
new file mode 100644
index 0000000..ec0b7aa
--- /dev/null
+++ b/gnu/packages/README_NO_AI.md
@@ -0,0 +1 @@
+This part of the guix-bioinformatics channel contains hand-crafted packages that were not written with the help of AI.