gendev: special machine for Pjotr

3 files changed, 139 insertions, 1 deletions

diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
index 6a691b8..8e65c90 100644
--- a/genenetwork/services/genenetwork.scm
+++ b/genenetwork/services/genenetwork.scm
@@ -294,8 +294,11 @@ object."
                               (source gn-sourcecode-directory)
                               (target source))
                              (file-system-mapping
-                              (source gn3-data-directory)
+                              (source genotype-files)
                               (target source))
+                             (file-system-mapping
+                              (source gn3-data-directory)
+                              (target source))    ; Rqtl usese this
                              (file-system-mapping ; GN2 and GN3 need to share TMPDIR
                               (source "/tmp")
                               (target "/tmp")
diff --git a/specials/gndev-deploy.sh b/specials/gndev-deploy.sh
new file mode 100755
index 0000000..c25df03
--- /dev/null
+++ b/specials/gndev-deploy.sh
@@ -0,0 +1,64 @@
+#! /bin/bash -e
+
+# This is a development machine used by Pjotr
+#
+# genenetwork-machines --- Guix configuration for genenetwork machines
+# Copyright © 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
+#
+# This file is part of genenetwork-machines.
+#
+# genenetwork-machines is free software: you can redistribute it
+# and/or modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of
+# the License, or (at your option) any later version.
+#
+# genenetwork-machines is distributed in the hope that it will be
+# useful, but WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with genenetwork-machines.  If not, see
+# <https://www.gnu.org/licenses/>.
+
+# See also https://issues.genenetwork.org/topics/systems/fire-up-genenetwork-system-container
+
+# this script should not be run as root.
+if [ "$EUID" -eq 0 ]
+  then echo "Please do not run as root." 
+  exit
+fi
+
+echo Build and install genenetwork gndev container on $HOSTNAME
+
+mkdir -p /export2/guix-containers/gndev/tmp
+rm -rf /export2/guix-containers/gndev/tmp/ # muck out
+touch /export2/guix-containers/gndev/tmp/gndev-tmp
+mkdir -p /export2/guix-containers/gndev/var/lib/acme
+mkdir -p /export2/guix-containers/genenetwork/etc/genenetwork
+mkdir -p /export2/data/gndev-xapian
+mkdir -p /export2/data/gndev-sqlite
+mkdir -p /export/data/gndev/genotype_files
+
+# Note that if you change these paths you need to rebuild the container
+container_script=$(~/opt/guix-gndev/bin/guix system container \
+                        --network \
+                        --load-path=.. -L ~/guix-bioinformatics \
+                        --verbosity=3 \
+                        --share=/export2/guix-containers/gndev/var/lib/acme=/var/lib/acme \
+                        --share=/export2/guix-containers/gndev/tmp=/var/tmp \
+                        --share=/export2/guix-containers/genenetwork/etc/genenetwork=/etc/genenetwork \
+                        --share=/export2/data/gndev-xapian \
+                        --share=/export2/data/gndev-sqlite \
+                        --expose=/export/data/genenetwork/genotype_files \
+                        --expose=/export/data/gndev \
+                        --share=/var/run/mysqld=/run/mysqld \
+                        --share=/export/source/gndev-debug \
+                        gndev.scm)
+
+name=/usr/local/bin/gndev-system-container
+if [ $? == 0 ] ; then
+  echo "Create $name -> $container_script"
+  sudo ln --force --symbolic $container_script $name
+  sudo ln --force --symbolic /usr/local/bin/$name /var/guix/gcroots
+fi
diff --git a/specials/gndev.scm b/specials/gndev.scm
new file mode 100644
index 0000000..440aedb
--- /dev/null
+++ b/specials/gndev.scm
@@ -0,0 +1,71 @@
+;;; genenetwork-machines --- Guix configuration for genenetwork machines
+;;; Copyright © 2022–2024 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2024 Pjotr Prins <pjotr.public01@thebird.nl>
+;;;
+;;; This file is part of genenetwork-machines.
+;;;
+;;; genenetwork-machines is free software: you can redistribute it
+;;; and/or modify it under the terms of the GNU General Public License
+;;; as published by the Free Software Foundation, either version 3 of
+;;; the License, or (at your option) any later version.
+;;;
+;;; genenetwork-machines is distributed in the hope that it will be
+;;; useful, but WITHOUT ANY WARRANTY; without even the implied
+;;; warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+;;; See the GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with genenetwork-machines.  If not, see
+;;; <https://www.gnu.org/licenses/>.
+
+(use-modules (gnu)
+             (genenetwork services genenetwork)
+             ((gnu packages admin) #:select (shepherd))
+             (gn services databases)
+             (gn packages genenetwork)
+             (gnu services databases)
+             (forge acme)
+             (forge nginx)
+             (forge socket))
+
+(operating-system
+  (host-name "gndev")
+  (timezone "UTC")
+  (locale "en_US.utf8")
+  (bootloader (bootloader-configuration
+               (bootloader grub-bootloader)
+               (targets (list "/dev/sdX"))))
+  (file-systems %base-file-systems)
+  (users %base-user-accounts)
+  (sudoers-file
+   (mixed-text-file "sudoers"
+                    "@include " %sudoers-specification
+                    "\nacme ALL = NOPASSWD: " (file-append shepherd "/bin/herd") " restart nginx\n"))
+  (packages %base-packages)
+  (services (cons* (service forge-nginx-service-type
+                            (forge-nginx-configuration
+                             (http-listen (forge-ip-socket
+                                           (ip "0.0.0.0")
+                                           (port 8990)))
+                             (https-listen (forge-ip-socket
+                                            (ip "0.0.0.0")
+                                            (port 8991)))))
+                   (service acme-service-type
+                            (acme-configuration
+                             (email "arunisaac@systemreboot.net")))
+                   (service genenetwork-service-type
+                            (genenetwork-configuration
+                             (genenetwork2 genenetwork2-stable)
+                             (genenetwork3 genenetwork3-stable)
+                             (server-name "gndev.genenetwork.org")
+                             (gn-auth-server-name "gndev-auth.genenetwork.org")
+                             (gn2-port 8992)
+                             (gn3-port 8993)
+                             (sql-uri "mysql://webqtlout:webqtlout@localhost/db_webqtl")
+                             (auth-db "/export2/data/gndev-sqlite/auth.db")
+                             (xapian-db "/export2/data/gndev-xapian")
+                             (genotype-files "/export/data/genenetwork/genotype_files")
+                             (sparql-endpoint "http://localhost:9092/sparql")
+                             (gn-sourcecode-directory "/export/source/gndev-debug")
+                             (gn3-data-directory "/export/data/genenetwork")))
+                   %base-services)))