Updated installation instructions and SERVER_PORT for single flask server

1 files changed, 51 insertions, 20 deletions

diff --git a/doc/README.org b/doc/README.org
index 5dc9e994..620c946c 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -12,13 +12,15 @@
    - [[#load-the-small-database-in-mysql][Load the small database in MySQL]]
  - [[#gn2-dependency-graph][GN2 Dependency Graph]]
  - [[#working-with-the-gn2-source-code][Working with the GN2 source code]]
+ - [[#running-elasticsearch][Running ElasticSearch]]
+   - [[#systemd][SystemD]]
+ - [[#read-more][Read more]]
  - [[#trouble-shooting][Trouble shooting]]
    - [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]]
-   - [[#error-can-not-find-directory-homegn2_data][ERROR: can not find directory $HOME/gn2_data]]
+   - [[#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype][ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype']]
    - [[#cant-run-a-module][Can't run a module]]
    - [[#rpy2-error-show-now-found][Rpy2 error 'show' now found]]
    - [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]]
- - [[#read-more][Read more]]
  - [[#irc-session][IRC session]]
 
 * Introduction
@@ -100,11 +102,13 @@ mysql (which comes as part of the GNU Guix genenetwork2 install).
 
 As root configure and run
 
-:  adduser mysql && addgroup mysql
-:  mysqld --datadir=/var/mysql --initialize-insecure
-:  mkdir -p /var/run/mysqld
-:  chown mysql.mysql ~/mysql /var/run/mysqld
-:  mysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048"
+#+BEGIN_SRC bash
+adduser mysql && addgroup mysql
+mysqld --datadir=/var/mysql --initialize-insecure
+mkdir -p /var/run/mysqld
+chown mysql.mysql ~/mysql /var/run/mysqld
+mysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048"
+#+END_SRC
 
 If you want to run as root you may have to set
 
@@ -192,6 +196,41 @@ http://biogems.info/contrib/genenetwork/gn2.svg
 
 See [[development.org]].
 
+* Running ElasticSearch
+
+In order to start up elasticsearch:
+Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch"
+
+
+** SystemD
+
+New server - as root run "systemctl restart elasticsearch"
+
+#+BEGIN_SRC
+tux01:/etc/systemd/system# cat elasticsearch.service
+[Unit]
+Description=Run Elasticsearch
+
+[Service]
+ExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch
+Environment=JAVA_HOME=/opt/jdk-9.0.4
+Environment="ES_JAVA_OPTS=-Xms1g -Xmx8g"
+Environment="PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin"
+LimitNOFILE=65536
+StandardOutput=syslog
+StandardError=syslog
+User=elasticsearch
+
+[Install]
+WantedBy=multi-user.target
+#+END_SRC
+
+* Read more
+
+If you want to understand the architecture of GN2 read
+[[Architecture.org]].  The rest of this document is mostly on deployment
+of GN2.
+
 * Trouble shooting
 
 ** ImportError: No module named jinja2
@@ -210,13 +249,17 @@ On one system:
 : export GEM_PATH="$HOME/.guix-profile/lib/ruby/gems/2.2.0"
 
 and perhaps a few more.
-** ERROR: can not find directory $HOME/gn2_data
+** ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype'
 
 The default settings file looks in your $HOME/gn2_data. Since these
 files come with a Guix installation you should take a hint from the
 values in the installed version of default_settings.py (see above in
 this document).
 
+You can use the GENENETWORK_FILES switch to set the datadir, for example
+
+: env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2
+
 ** Can't run a module
 
 In rare cases, development modules are not brought in with Guix
@@ -257,18 +300,6 @@ if that works run genenetwork after setting SQL_URI to something like
 
 : export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s
 
-* Running ElasticSearch
-
-In order to start up elasticsearch:
-Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch"
-
-New server - as root run "systemctl restart elasticsearch"
-
-* Read more
-
-If you want to understand the architecture of GN2 read
-[[Architecture.org]].  The rest of this document is mostly on deployment
-of GN2.
 
 * IRC session