From baeafc5ccc4a9893d22e6629db97720e3fa6d3ae Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 3 Dec 2023 09:47:38 -0600
Subject: Rename/move

---
 topics/genenetwork/starting_gn1.gmi | 102 ++++++++++++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 topics/genenetwork/starting_gn1.gmi

(limited to 'topics/genenetwork/starting_gn1.gmi')

diff --git a/topics/genenetwork/starting_gn1.gmi b/topics/genenetwork/starting_gn1.gmi
new file mode 100644
index 0000000..efbfd0f
--- /dev/null
+++ b/topics/genenetwork/starting_gn1.gmi
@@ -0,0 +1,102 @@
+# Starting GN1
+
+The GN1 repos are at
+
+=> https://github.com/genenetwork/genenetwork1
+
+Branches are:
+
+* master: my main branch - used in pjotr-test
+* lily: running but almost discontinued
+* production: on tux01
+
+Note that there are some hard coded paths/IPs - so simply merging is not a great idea.
+
+On tux01 GN1 is running inside a Guix container.
+
+Start a screen and run the guix deploy script. See the README file in
+
+gn1@tux01:~/production/gnshare/gn
+
+# Guix
+
+At this point GN1 is fixed at Feb 2021:
+
+guix: 1.2.0-12.dffc918
+guix-past: 159be3d7e86e1f22b2b7b1efc938ed63120dc973
+guix-bioinformatics: 697a66bf0e897a101e8e3cefbaf250491039fe93
+
+# Building
+
+On an update of guix the build may fail. Try
+
+```
+~/opt/guix-gn1/bin/guix build
+    -L /home/gn1/guix-past/modules/ \
+    -L /home/gn1/guix-bioinformatics/ \
+    genenetwork1
+```
+
+## Updating mariadb connection on lily
+
+```
+   restart apache in lily
+   [root@lily base]# /etc/init.d/httpd restart
+   Stopping httpd:                                            [  OK  ]
+   Starting httpd:                                            [  OK  ]
+   [root@lily base]# pwd
+   /gnshare/gn/web/webqtl/base
+   [root@lily base]#
+   /gnshare/gn/web/webqtl/base/webqtlConfigLocal.py
+   #######################################'
+   #      Environment Variables - private
+   #########################################
+   # sql_host = '[1]tux02.uthsc.edu'
+   # sql_host = '128.169.4.67'
+   sql_host = '172.23.18.213'
+   SERVERNAME = sql_host
+   MYSQL_SERVER = sql_host
+   DB_NAME = 'db_webqtl'
+   DB_USER = 'x'
+   DB_PASSWD = 'x'
+   MYSQL_UPDSERVER = sql_host
+   DB_UPDNAME = 'db_webqtl'
+   DB_UPDUSER = 'x'
+   DB_UPDPASSWD = 'x'
+   GNROOT = '/gnshare/gn/'
+   PythonPath = '/usr/bin/python'
+   PIDDLE_FONT_PATH =
+   '/usr/lib/python2.4/site-packages/piddle/truetypefonts/'
+```
+
+SQL may also need to be updated here:
+
+=> /gnshare/gn/web/webqtl/base/webqtlConfigLocal.py
+=> /gnshare/gn/web/infoshare/includes/config.html
+=> /gnshare/gn/web/infoshare/includes/db.inc
+
+## Updating from lily
+
+Git sync
+
+```
+gn1@tux01:~/production/gnshare/gn-pjotr-test$
+git checkout lily
+git pull pjotr@lily.genenetwork.org:/gnshare/gn/
+```
+
+Menu sync
+
+```
+gn1@tux01:~/production/gnshare/gn-pjotr-test$
+scp pjotr@lily.genenetwork.org:/gnshare/gn/web/javascript/*.js web/javascript/
+git status
+```
+
+## Updating httpd.conf
+
+To update the httpd.conf you need to edit the system file in guix-bioinformatics. It can be built with
+
+```
+guix build -L ~/guix-past/modules/ -L ~/guix-bioinformatics/ -e '(@ (gn services gn1-httpd-config) GN1-httpd-config)'
+```
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