From 7af301caa7d8a5f01e7e3be007e4ba53dc482eee Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 18 Nov 2024 14:41:52 -0600
Subject: Update invocation documentation. Remove unnecessary scripts/manifest

Since we can now use the package file, we no longer need the
invocation scripts we used before, or the manifest I'd written.
---
 .guix-shell     |  7 -------
 README.md       |  7 ++-----
 manifest.scm    | 23 -----------------------
 web/.guix-shell |  8 --------
 4 files changed, 2 insertions(+), 43 deletions(-)
 delete mode 100755 .guix-shell
 delete mode 100644 manifest.scm
 delete mode 100644 web/.guix-shell

diff --git a/.guix-shell b/.guix-shell
deleted file mode 100755
index bc81e06..0000000
--- a/.guix-shell
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-#
-#  . .guix-shell -- guile -L . --fresh-auto-compile --listen=1970
-
-echo "Create a shell to run tools."
-
-guix shell  -L ~/guix-bioinformatics -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel tar xz python python-lmdb python-cffi guile-gcrypt guile-hashing time gemma-gn2 $*
diff --git a/README.md b/README.md
index 1f3b62a..d3326bd 100644
--- a/README.md
+++ b/README.md
@@ -28,13 +28,10 @@ git clone tux02.genenetwork.org:/home/git/public/gn-guile
 GNU Guile allows you to develop against a live running web server using emacs-geiser. To try this fire up the web server from the `web` directory as
 
 ```sh
-cd web
-unset GUIX_PROFILE
-. .guix-shell -- guile -L .. --fresh-auto-compile --listen=1970 -e main ./webserver.scm 8091
+guix shell --container --network --file=guix.scm -- guile -L . --fresh-auto-compile --listen=1970 -e main web/webserver.scm 8091
 ```
 
-Note the leading dot. The .guix-shell is defined in `gn-guile/web` and loads required packages using GNU Guix.
-If you are on Debian you may need to unset GUIX_PROFILE first.
+The `--container` option runs the code in an isolated container, and the `--network` option connects that container's networking to the host to allow you to access the running service.
 
 ## Welcome to the world of interactive Lisp programming
 
diff --git a/manifest.scm b/manifest.scm
deleted file mode 100644
index 80b15ee..0000000
--- a/manifest.scm
+++ /dev/null
@@ -1,23 +0,0 @@
-(specifications->manifest
- '("coreutils"
-   "guile"
-   "guile-dbi"
-   "guile-dbd-mysql"
-   "guile-fibers"
-   "guile-json"
-   "guile-gnutls"
-   "guile-readline"
-   "guile-redis"
-   "openssl"
-   "nss-certs"
-   "gemma"
-   "parallel"
-   "tar"
-   "xz"
-   "python"
-   "python-lmdb"
-   "python-cffi"
-   "guile-gcrypt"
-   "guile-hashing"
-   "time"
-   "gemma-gn2"))
diff --git a/web/.guix-shell b/web/.guix-shell
deleted file mode 100644
index b4aee2a..0000000
--- a/web/.guix-shell
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-#
-#  run with options '-- ./webserver.scm 8091' e.g.
-#  . .guix-shell -- guile -L .. --fresh-auto-compile --listen=1970 -e main ./webserver.scm 8091
-
-echo "Note run: running web-server"
-
-guix shell guile guile-commonmark guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs $*
-- 
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