{"action":"created","comment":{"url":"https://api.github.com/repos/TGAC/miso-lims/pulls/comments/65908914","id":65908914,"diff_hunk":"@@ -17,221 +16,46 @@ MISO: An open source LIMS for small-to-large scale sequencing centres\n >\n > You should have received a copy of the GNU General Public License\n > along with MISO.  If not, see <http://www.gnu.org/licenses/>.\n->\n-> You can follow MISO development on Twitter: @misolims (https://twitter.com/misolims), @froggleston (https://twitter.com/froggleston)\n-\n-For Full MISO Documentation please visit our documentation website:\n-https://documentation.tgac.ac.uk/display/MISO/MISO+Documentation+Home\n-\n-\n-VERSION 0.2.0 (Neon)\n-\n-1) BUILDING\n------------\n-\n-You will need [Maven 3.0.5] [3] to build MISO (*NOTE Not Maven 2!*). Once you have grabbed the code and installed Maven, in the root of the project (you should see a pom.xml file and module directories like `analysis-server` and `core` etc) call:\n-\n-    mvn clean install -P external\n-\n-This will *NOT* run unit tests. To enable unit tests of database sanity, use:\n-\n-    mvn -DsqlTests=true install -P external\n-\n-In order for the tests to work, you will need a MISO database set up as per the instructions below, and the correct properties specified in `sqlstore/src/test/resources/test.db.properties`.\n-\n-All being well after a few minutes (it can take a while to download all the required artifacts given the speed of your connection), you should see `BUILD SUCCESSFUL`.\n-\n-2) UPGRADING\n-------------\n-\n-If you are upgrading from a previous version of MISO, you will need to follow these steps:\n-\n-* Backup your existing database\n-* Stop Tomcat\n-* Set a baseline for flyway (assuming you have only applied base_schema and miso_type_data patches) using `cd sqlstore && mvn flyway:baseline -Dflyway.baselineVersion=2 -Dflyway.baselineDescription=\"Base version\"`\n-* Update the database using `cd sqlstore && mvn -P external compile flyway:migrate`\n-* Delete (or move) the old `<tomcat>/webapps/ROOT.war`\n-* Delete the `<tomcat>webapps/ROOT` directory\n-* Copy the newly built `miso-web/target/ROOT.war` to `<tomcat>/webapps`\n-* Restart Tomcat\n-\n-Done!\n-\n-3) INSTALLING\n--------------\n-\n-3.1 ) Setting up the MISO database\n-\n-You will need to install MySQL v5 or greater. Log in to your local MySQL install, and create a database called 'lims':\n-\n-    CREATE DATABASE lims;\n-    USE lims;\n-\n-Then add a user that has all grant access on the 'lims' db:\n-\n-    GRANT ALL ON `lims`.* TO 'tgaclims'@'localhost';\n-    GRANT ALL ON `lims`.* TO 'tgaclims'@'localhost' IDENTIFIED BY 'tgaclims';\n-\n-If your database and Tomcat install are on different machines, then you will obviously need to add a grant privilege to the MISO\n-database from your remote machine:\n-\n-    GRANT ALL ON `lims`.* TO 'tgaclims'@'your.tomcat.install.server';\n-    GRANT ALL ON `lims`.* TO 'tgaclims'@'your.tomcat.install.server' IDENTIFIED BY 'tgaclims';\n-\n-Then populate the database with the two dumps by running the following commands at a shell prompt:\n-\n-    cd sqlstore && mvn -P external compile flyway:migrate\n-\n-The database schema many need to be upgraded in future version. This command\n-will apply the necessary changes to update an existing database.\n-\n-3.2 ) Setting up the MISO web application\n-\n-You will need a suitable Java web application container, such as Tomcat 7.x (http://tomcat.apache.org/download-70.cgi),\n-to deploy MISO. Once Tomcat has been installed, download the latest MISO WAR file. The latest WAR file can be found here:\n-\n-https://repos.tgac.ac.uk/miso/latest/ROOT.war\n-\n-If you're the thrill-seeking type, nightly builds from the develop branch which are \"bleeding edge\" can be found here, following the format ROOT-{version}_{buildNumber}_{revision}.war:\n-\n-https://repos.tgac.ac.uk/miso/nightly/\n-\n-Copy this file to your `<tomcat-install>/webapps/` directory. DO NOT START TOMCAT YET. Instead, follow the configuration steps below.\n-\n-4 ) CONFIGURATION\n------------------\n-\n-MISO is configured using the Tomcat context xml system, the main miso.properties file that resides in the\n-`<tomcat-install>/webapps/ROOT/WEB-INF/classes` directory, and properties files that live in the default MISO storage directory.\n-\n-Make sure that these options are correct for your system at the time of container startup.\n-\n-4.1 ) Setting the database environment\n-\n-MISO uses JNDI (Java Naming and Directory Interface) to configure the connection to the underlying MySQL database that you set\n-up in the step 1.1. To configure Tomcat to manage the JNDI datasource, please create a file called `ROOT.xml` in the following\n-directory `<tomcat-install>/conf/Catalina/localhost` and populate it with the following information:\n-\n-    <Context path=\"/ROOT\" docBase=\"${catalina.home}/webapps/ROOT\" debug=\"1\">\n-      <Resource name=\"jdbc/MISODB\" type=\"javax.sql.DataSource\"\n-      driverClassName=\"com.mysql.jdbc.Driver\"\n-      initialSize=\"32\"\n-      maxIdle=\"10\"\n-      maxActive=\"100\"\n-      maxWait=\"1000\"\n-      removeAbandoned=\"true\"\n-      removeAbandonedTimeout=\"120\"\n-      logAbandoned=\"true\"\n-      testWhileIdle=\"true\"\n-      testOnBorrow=\"true\"\n-      testOnReturn=\"true\"\n-      validationQuery=\"select 1\"\n-      url=\"jdbc:mysql://localhost:3306/lims?autoReconnect=true&amp;zeroDateTimeBehavior=convertToNull&amp;useUnicode=true&amp;characterEncoding=UTF-8\"\n-      username=\"tgaclims\"\n-      password=\"tgaclims\"/>\n-\n-     <Resource name=\"file/CONAN_PROPERTIES\" type=\"java.util.File\"\n-                factory=\"uk.ac.ebi.fgpt.naming.factory.FileFactory\"\n-                 path=\"../webapps/ROOT/WEB-INF/conan.properties\"/>\n-\n-     <!-- uncomment if using the Stats DB -->\n-     <!--\n-     <Resource name=\"jdbc/STATSDB\" type=\"javax.sql.DataSource\"\n-      driverClassName=\"com.mysql.jdbc.Driver\" initialSize=\"32\" maxIdle=\"32\" maxActive=\"100\" maxWait=\"-1\"\n-      url=\"jdbc:mysql://your_stats_db_server:3306/run_statistics?zeroDateTimeBehavior=convertToNull&amp;useUnicode=true&amp;characterEncoding=UTF-8\"\n-      username=\"statsuser\"\n-      password=\"statspass\"/>\n-      -->\n-    </Context>\n-\n-If the `<tomcat-install>/conf/Catalina/localhost` directory doesn't exist (usually due to a fresh Tomcat install), either create\n-it yourself, or cycle a Tomcat startup/shutdown and it should appear.\n-\n-If your Tomcat install has the autoDeploy=\"true\" flag set in server.xml, if you delete the `webapps/ROOT` directory and the ROOT.war\n-file, Tomcat will delete the context ROOT.xml file. Either set autoDeploy to false, and manually deploy your webapp, or make\n-the ROOT.xml file undeletable by using 'chattr +i' ('chattr -i' will undo this operation). See: https://issues.apache.org/bugzilla/show_bug.cgi?id=40050\n-\n-Again, if your database and Tomcat install are on different machines, then you will need to change the connection URL above to\n-the name of your remote database server:\n-\n-    url=\"jdbc:mysql://your.database.server:3306/lims\"\n-\n-You will need to copy the mysql connector library and the JNDI File Factory library to your Tomcat install to ensure the JNDI system can see the MISO database.\n-Grab the jar files from:\n-\n-https://repos.tgac.ac.uk/miso/common/mysql-connector-java-5.1.10.jar\n-\n-https://repos.tgac.ac.uk/miso/common/jndi-file-factory-1.0.jar\n-\n-And copy them to <tomcat-install>/lib/\n-\n-4.2 ) Setting up miso.properties file\n-\n-The main miso.properties file is located in the `<tomcat-install>/lib/classes/` directory.\n-\n-The miso.properties file specifies a number of general options. The only option that needs attention is `miso.baseDirectory`.\n-Please set this to the absolute path of where you would like MISO to store files on disk, i.e. logs, uploaded files, etc.\n-\n-The default path is `/storage/miso`. It is recommended that create this path on disk and that you do not change this location as some things will break.\n-\n-> NB: You shouldn't need to change the miso.properties file as long as the /storage/miso directory exists on your filesystem and is writeable!\n-\n-4.3 ) Setting up userspace properties\n-\n-MISO achieves userspace configuration via extra properties files kept in the storage directory specified by the `miso.baseDirectory`\n-property (see 2.2 above). Default versions of these files are available here:\n-\n-https://repos.tgac.ac.uk/miso/latest/miso_userspace_properties.tar.gz\n-\n-Unpack this file to your MISO storage directory, which again is `/storage/miso` by default. You should see 4 files:\n-\n-* issuetracker.properties - settings for an issue tracking system, such as JIRA or RT.\n-* mail.properties - email settings so that MISO can send emails to users.\n-* security.properties - properties to set the security environment (see 2.4 below).\n-* submission.properties - properties to set the submission environment (see 2.5 below).\n-\n-4.4 ) Setting the security environment\n-\n-MISO can use either LDAP or SQL as an authentication mechanism, and will need to know where your chosen method resides. These\n-properties need to be set before the container is started, and relate to properties files stored on disk.\n-\n-Firstly, the security options for both auth systems are specified in the `security.properties` file. If you are using JDBC,\n-then it is unlikely that you will need to change any options, but the LDAP setup is far more complex.\n-Please ask your sysadmin to match up the MISO LDAP options with your local LDAP server options.\n-\n-Secondly, the `security.method` environment property relates to the security mechanism, i.e. 'ldap' or 'jdbc', where 'ldap' auths\n-against an LDAP server, and 'jdbc' auths against a local database (usually the MISO database itself). Please use 'jdbc' if you\n-are unsure. There is a default admin user that is shipped with the MISO database, and the username/password login is admin/admin.\n-\n-To set the `security.method` property, use local environment variables on Tomcat startup. Please see the \"Starting MISO\" section below.\n-\n-> NB: You are likely to see startup errors like the one below if you do not set this property, and start Tomcat as outlined in section 3!\n-\n-> 20-Oct-2010 11:08:28 org.apache.catalina.core.StandardContext start\n-\n-> SEVERE: Error listenerStart\n \n-> 20-Oct-2010 11:08:28 org.apache.catalina.core.StandardContext start\n+View [Full MISO Documentation](https://documentation.tgac.ac.uk/display/MISO/MISO+Documentation+Home)\n \n-> SEVERE: Context [/tgac] startup failed due to previous errors\n+## Trying MISO\n+The simplest way to get MISO up and running quickly is to use our virtual\n+machine image with everything preinstalled. A VirtualBox instance is available\n+with a self-contained MISO installation and MySQL database server, fully\n+configured and can be used out-of-the-box.\n \n-4.5 ) Submission properties\n+To use it:\n \n-MISO is able to submit sequence data to the major sequence archives, i.e. the SRA at the EBI, and the EMBL GenBank. Currently,\n-only ERA submissions are supported out-of-the-box. The settings for these services are specified in the `submission.properties` file.\n+1.  Download VirtualBox software from: [https://www.virtualbox.org/](https://www.virtualbox.org/)\n+1.  Download the MISO OVA: [https://repos.tgac.ac.uk/miso/latest/MISO_Image.ova](https://repos.tgac.ac.uk/miso/latest/MISO_Image.ova)\n+1.  Import this OVA file into VirtualBox via _File_ → _Import Appliance_. You may have to select _Bridged Adaptor_ instead of _NAT_ in the network settings.\n+1.  Start the instance. Starting the appliance will result in an Ubuntu virtual machine complete with all MISO’s prerequisites pre-installed. The login for the virtual image is `miso` / `misoadmin`.\n+1.  Start MISO server by using `./misoStart.sh` and then open the browser and go http://localhost:8090/\n+1.  Log in to MISO using `admin` / `admin`. Only some simple configuration for certain elements is required, such as _Sequencer References_, Printers and any additional users and groups.\n \n-5 ) STARTING MISO\n------------------\n+## Running an Instance of MISO\n+To run your own MISO instance in the long term, you will need to maintain your\n+own fork of the MISO codebase with your configuration changes. For each\n+release, you will need to merge the main changes into your local repository and\n+then deploy a new version.\n \n-To set the `security.method` property to use the local MISO database and start the Tomcat instance, run the following command, which will use the JDBC security.method and assign 768MB RAM to the Java heap:\n+For deployment, you will need a mySQL database server, a server to scan the\n+sequencer output directories (the notification server), and a Tomcat\n+application server. These can be on the same machine. It is advisable to\n+have a separate build environment.\n \n-    cd <tomcat-install>/bin/\n-    JAVA_OPTS=\"$JAVA_OPTS -Dsecurity.method=jdbc -Xmx768M\" ./startup.sh\n+At each upgrade, there are two steps: migrating the database and deploying a\n+new application. Each version of the application contains all the migrations\n+needed to upgrade any old database to match the current version. However, there\n+is no rollback procedure, so a full database backup should be taken before\n+migration.\n \n-All going well, you should be able to go to http://localhost:8080/ and log in to MISO using the admin/admin username and password combination.\n+Installation and configuration details can be found in the [MISO maintainer guide](admin-manual.md).\n \n-> NB: Please remember that if you need to set any properties in the userspace properties files, you will need to make sure that you stop Tomcat, make the changes and then restart it.\n+## Demo Version\n+This needs to be done.\n \n-  [1]: http://www.tgac.ac.uk/        \"TGAC\"\n-  [2]: http://www.tgac.ac.uk/miso/  \"MISO\"\n-  [3]: http://maven.apache.org/download.html    \"Maven\"\n+## Contact and Community\n+[MISO Twitter](https://twitter.com/misolims)\n+[Slack 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