From 02a6d9ebc2e2c160874e2f52412cfc7be67b7231 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 21 Jun 2024 05:49:56 -0500
Subject: genecup: updated information - now running as a container

---
 issues/genecup-running-as-root.gmi                 |  6 ++++-
 .../per-service-profile-for-shepherd-services.gmi  | 15 ++++++++---
 topics/deploy/genecup.gmi                          | 30 ++++++++++++++++++++++
 3 files changed, 47 insertions(+), 4 deletions(-)
 create mode 100644 topics/deploy/genecup.gmi

diff --git a/issues/genecup-running-as-root.gmi b/issues/genecup-running-as-root.gmi
index c48924f..72d5704 100644
--- a/issues/genecup-running-as-root.gmi
+++ b/issues/genecup-running-as-root.gmi
@@ -1,5 +1,9 @@
 # genecup is currently running as root on penguin2.
 
+Is this still true for tux02? Fixed: genecup is now running as a container so we can close this.
+
+## Info
+
 Currently when run using shepherd it fails like this:
 
 guix system: warning: Consider running 'guix pull' followed by
@@ -32,7 +36,7 @@ A number of changes to different types of shepherd services (exec-command, make-
 * assigned: Efraim
 * type: failure
 * keywords: genecup, penguin2
-* status: unclear
+* status: closed
 * priority: high
 
 ## Notes
diff --git a/issues/per-service-profile-for-shepherd-services.gmi b/issues/per-service-profile-for-shepherd-services.gmi
index 654a723..43c9118 100644
--- a/issues/per-service-profile-for-shepherd-services.gmi
+++ b/issues/per-service-profile-for-shepherd-services.gmi
@@ -1,11 +1,17 @@
 # Each shepherd service needs its own guix profile.
 
-Currently there are a bunch of shepherd services (on Penguin2, as user shepherd) who are using the global shepherd guix profile and loading guix-bioinformatics at service start time to start their services. This is bad because:
+UPDATE: genecup is now running as a container on tux02. This is a model for getting rid of guix profiles. Note that we
+do need to fixate guix-bioinformatics and guix-past channels *per* service. Otherwise updates are impossible.
+
+In time we may move to hosting these services in a guix system container (a VM).
+
+Currently there are a bunch of shepherd services (on tux02, as user shepherd) who are using the global shepherd guix profile and loading guix-bioinformatics at service start time to start their services. This is bad because:
 
 * we aren't using per-service guix-bioinformatics worktrees, so the branch changes between service refreshes
 * service start times are high because we have to rebuild the service (due to above)
 * services which are restarted are in an "untested" state until they work
 
+
 ## Services which need to be migrated:
 
 * covid19-pubseq (uses shared (broken!) guix profile, uses shared config directory)(currently running by hand by Pjotr)
@@ -22,6 +28,9 @@ Currently there are a bunch of shepherd services (on Penguin2, as user shepherd)
 
 ## Services which already have their own profile:
 
+Note that the profiles essentially just contain the guix binary, acting like a time machine. It is
+used to fire up a guix shell/environment:
+
 * bnw
 * cronjob-gitea
 * cronjob-pubmed (genecup)
@@ -34,8 +43,8 @@ Currently there are a bunch of shepherd services (on Penguin2, as user shepherd)
 
 ## Tags
 
-* assigned: efraim
+* assigned: efraim, pjotrp
 * type: bug
-* status: unclear
+* status: in progress
 * priority: high
 * keywords: shepherd, system administration
diff --git a/topics/deploy/genecup.gmi b/topics/deploy/genecup.gmi
new file mode 100644
index 0000000..2054844
--- /dev/null
+++ b/topics/deploy/genecup.gmi
@@ -0,0 +1,30 @@
+# Deploying genecup
+
+On Tux02 as shepherd user I can build:
+
+```
+./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 24 -M 8
+```
+
+To run genecup in a container we have a trick to include the source code by cd'ing into the built version
+
+```
+export EDIRECT_PUBMED_MASTER=/export2/PubMed
+export TMPDIR=/export/ratspub/tmp
+export NLTK_DATA=/export2/PubMed/nltk_data
+
+# This version for the genecup guix profile which includes guix-bioinformatics, using genecup-channels.scm.
+# shepherd@tux02:~/services/genecup$ ./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 24 -M 8
+
+cd /home/shepherd/services/genecup
+cd $(/home/shepherd/services/genecup/guix/bin/guix build -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 4)
+
+/home/shepherd/services/genecup/guix/bin/guix shell -C -N --expose=/etc/ssl/certs --expose=$EDIRECT_PUBMED_MASTER --share=$TMPDIR -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native coreutils-minimal -- env TMPDIR=$TMPDIR EDIRECT_PUBMED_MASTER=$EDIRECT_PUBMED_MASTER NLTK_DATA=$NLTK_DATA ./server.py
+```
+
+That means you can also develop software running in a container with the last command by switching into a repo:
+
+```
+cd $repo
+run last command using guix shell
+```
-- 
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