Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 1/24 PhenotypeDatabase / GSCF
How to install dbNP/GSCF with java 8, tomcat 8, Apache, PostgreSQL 9.5 On CentOS 7 / RHEL 7
This tutorial builds heavily on the instructions that can be found on the PhenotypeDatabase github page https://github.com/PhenotypeFoundation/PhenotypeDatabase#installation
Finn Sandø Department of Nutrition, Exercise and Sports (NEXS) University of Copenhagen
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 2/24 PhenotypeDatabase / GSCF
Introduction
In this tutorial it is assumed that you are logged in to a freshly installed CentOS 7 or RHEL 7 server (Redhat Enterprise Linux - RHEL).
l will go through installing and configuring:
Java 8 – I will show how to install java both from the distribution repository and directly from Oracle
Tomcat 8 – java application server
Apache – web server (will act as web facing front end) mod_jk – a necessary component for Apache not natively supported by Redhat that needs to be compiled
PostgreSQL 9.5 – The latest version of postgres
Virtual hosts – the dbNP website (mostly copy-paste from the PhenotypeDatabase github page) dbNP/GSCF – the main java application itself
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Installing a few utilities First a few utilities are needed. In order to download files I will use the program ”wget” and in order to edit text files I will use the text editor ”nano”.
Most of the commands in this tutorial need to be executed as ”root”, so the easiest is to just ”become root” by this: sudo su To install progams in CentOS/Redhat you use the package manager ”yum” Type this to install ”wget” and ”nano” yum install wget nano
When using the nano editor use ctrl+o to save and ctrl+x to leave
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Installing java 8 – from repository To install from the repository is simple yum install java-1.8.0-openjdk yum install java-1.8.0-openjdk-devel To check the installation java -version whereis java which java
Installing java 8 – from Oracle It may sometimes be needed to use one of the versions provided directly from Oracle
First go to Oracle’s website to find the latest version of java http://www.oracle.com/technetwork/java/javase/downloads
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Scroll down, find and click the ”jre” button
Accept the licence agreement
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Find the linux-x86 "rpm" version This is the version for RHEL and CentOS. Note the address, in this case http://download.oracle.com/otn-pub/java/jdk/8u92-b14/jre-8u92-linux-x64.rpm
To download java into the current folder use wget, type (or copy) the following to the command line wget --no-cookies --no-check-certificate \ --header "Cookie: gpw_e24=http://www.oracle.com/; \ oraclelicense=accept-securebackup-cookie" \ "http://download.oracle.com/otn-pub/java/jdk/8u92-b14/jdk-8u92-linux-x64.rpm"
After the file is successfully downloaded type this to install rpm -ivh jdk-8u92-linux-x64.rpm
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 7/24 PhenotypeDatabase / GSCF
Installing Tomcat 8 In this part I wil Find and download latest version of Tomcat from the Tomcat site Install Tomcat into the /opt folder Prepare the system for Tomcat Configure Tomcat
First, in order to get the lastest version go to the tomcoat.org site
http://tomcat.apache.org/download-80.cgi
Scroll down to the latest version, not the address in this case http://ftp.download-by.net/apache/tomcat/tomcat-8/v8.0.33/bin/apache-tomcat-8.0.33.tar.gz
To download tomcat files into the current folder wget http://ftp.download-by.net/apache/tomcat/tomcat-8/v8.0.33/bin/apache-tomcat-8.0.33.tar.gz
Unpack (this will unpack the downloaded file into a folder "apache-tomcat-8.0.33")
tar xzf apache-tomcat-8.0.33.tar.gz
Move the Tomcat files into the /opt folder
mv apache-tomcat-8.0.33 /opt/
Go the /opt folder, in order to standardize access to Tomcat create a symbolic link to the Tomcat folder
cd /opt ln -s apache-tomcat-8.0.33 tomcat
List the content of /opt
ls –l
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 8/24 PhenotypeDatabase / GSCF drwxr-xr-x. 10 tomcat tomcat 4096 Apr 27 18:30 apache-tomcat-8.0.33 lrwxrwxrwx 1 root root 20 Apr 26 18:39 tomcat -> apache-tomcat-8.0.33
Prepare the system for Tomcat First we need to add a tomcat user and a tomcat group, tell the system that this user’s home dir is /opt/tomcat and, for security reasons, disallow this user login rights. add tomcat user groupadd tomcat sudo useradd -M -s /bin/nologin -g tomcat -d /opt/tomcat tomcat
Next the permissions on the /opt/tomcat folder need to be set Under normal operation the Tomcat user only needs to be able to change a few config files. Therefore the most secure setup is to make ”root” owner of everything execpt for these few files.
Set all files in the /opt folder to be owned by root cd /opt chown root:root . -R
Allow the tomcat user to change a few config files cd tomcat chgrp -R tomcat conf chmod g+rwx conf chmod g+r conf/* chown -R tomcat webapps/ work/ temp/ logs/
Sometimes during setup, however, this can be a problem making it necessary to give tomcat full rights cd /opt chown tomcat:tomcat . -R
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 9/24 PhenotypeDatabase / GSCF
Next we need to create startup scripts so the CentOS/RHEL server can start Tomcat This wil create a systemd unit script to start Tomcat nano /etc/systemd/system/tomcat.service
The content of the tomcat.service file
# Systemd unit file for tomcat [Unit] Description=Apache Tomcat Web Application Container After=syslog.target network.target
[Service] Type=forking
Environment=JAVA_HOME=/usr/lib/jvm/jre Environment=CATALINA_PID=/opt/tomcat/temp/tomcat.pid Environment=CATALINA_HOME=/opt/tomcat Environment=CATALINA_BASE=/opt/tomcat Environment='CATALINA_OPTS=-Xms512M -Xmx1024M -server -XX:+UseParallelGC' Environment='JAVA_OPTS=-Djava.awt.headless=true -Djava.security.egd=file:/dev/./urandom'
ExecStart=/opt/tomcat/bin/startup.sh ExecStop=/bin/kill -15 $MAINPID
User=tomcat Group=tomcat
[Install] WantedBy=multi-user.target
To start Tomcat, first reload the systemd daemon, start Tomcat (to see that it actually starts). If successful, make the startup happen automatically in the future (enable). systemctl daemon-reload systemctl start tomcat systemctl enable tomcat
Finally we need to open the firewall for port 80 and port 8080 firewall-cmd --add-port=80/tcp --permanent firewall-cmd --add-port=8080/tcp --permanent firewall-cmd --reload
Tomcat is now installed and running and should be reachable on ”your-domain:8080”
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Configuring Tomcat Next step is to configure tomcat. Tomcat will work fine without further configuration but an administrator may find it useful to have access to Tomcat’s manager interface (”manager-gui” or ”Manager App”).
To get access to the Manager App you need to add a user with admin rights to the manager-gui.
Edit the ”tomcat-users.xml” file nano /opt/tomcat/conf/tomcat-users.xml
Create a user with suitable permissions by adding these lines between the
The complete the ”tomcat-users.xml” file
After the changes have been saved, restart Tomcat systemctl restart tomcat
It should now be possible to login to the Tomcat Manager App by going to http://mydomain:8080/ Try to click the ”Manager App” button
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Now login with the username and password defined in the ”tomcat-users.xml” file
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 13/24 PhenotypeDatabase / GSCF increase the allowed size of uploaded files One last Tomcat configuration that may be needed is to increase the allowed size of uploaded files.
There are several different ways to install a java web application in Tomcat: First there is the completely manual approach that I am going to show in this tutorial, then there is a semi-manual where you place the installation file in the correct place and let Tomcat handle the final steps and finally you can, via the Manager App, upload a web application directly from your desktop to the server.
Unfortunately by default the maximum allowed file size is 50mb but the PhenotypeDatabase is almost 100mb, so when you try to upload it the installation will fail, and the error message may not be obvious.
In order to fix this issue you will have to increase the maximum allowed size of uploaded files. This setting is in the ” manager/WEB-INF/web.xml”
nano /opt/tomcat/webapps/manager/WEB-INF/web.xml
In this file look for this part
...
...
After the changes have been applied, restart Tomcat systemctl restart tomcat
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Installing PostgreSQL 9.5
CentOS 7 / RHEL 7 by default supports postgres 9.2. To get the most recent version you need to use the repositories maintained by the Postgres Organization at http://postgresql.org
The process of installing PostgreSQL is to first install the repository and then using the package manager to install postgres
Install the repository rpm -Uvh http://yum.postgresql.org/9.5/redhat/rhel-7-x86_64/pgdg-centos95-9.5-2.noarch.rpm
Then install PostgreSQL yum install postgresql95-server postgresql95-contrib
After successful installation the database must be initialized by running this script
/usr/pgsql-9.5/bin/postgresql95-setup initdb
Start postgres and make it start automatically systemctl start postgresql-9.5 systemctl enable postgresql-9.5
The program to access postgres is ”psql”. In order to be able to access the server you need to make some changes to the postgres user permissions in the ”pg_hba.conf” file.
nano /var/lib/pgsql/9.5/data/pg_hba.conf
In this file change the ”peer” and ”ident” options for the rows ”local” and ”127.0.0.1/32” (those both concern logins that are coming from the server itself) to ”trust” and ”md5” respectively.
... # TYPE DATABASE USER ADDRESS METHOD
# "local" is for Unix domain socket connections only local all all trust # peer # IPv4 local connections: host all all 127.0.0.1/32 md5 # ident ...
Save the file and restart postgres systemctl restart postgresql-9.5
It is now possible to login to postgres with this command (type ”\q” to leave) psql -U postgres -d postgres
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Creating the database to be used by dbNP/GSCF First login to postgres psql -U postgres -d postgres
Now create a database user and the database that will be used by the dbNP/GSCF application.
CREATE USER gscfuser WITH PASSWORD 'secret-pw'; CREATE DATABASE gscfwww WITH OWNER gscfuser; GRANT ALL PIVILEGES ON DATABASE gscfwww TO gscfuser;
Please note one important difference compared to the documentation on the PhenotypeDatabase github page: Here I use the database name ”gscfwww” (rather than ”gscf-www” with a dash). The reason is that while this is not important per se, dash in database names is non-standard and will force the use of double quotes in sql-queries every time the database is mentioned, which can be quite inconvenient if direct dealing wth database should be needed.
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Installing Apache web server
Before installing Apache there is a module mod_jk, which helps in conncecting between the Tomcat and Apache, that is not available on CentOS/RHEL. This module needs to compiled specifically.
Download, compile and Install mod_jk
Install the Apache server and the development files necessary for compiling mod_jk yum install httpd httpd-devel gcc gcc-c++ make libtool
Download and unpack the source code for mod_jk mkdir mod-jk cd mod-jk wget http://www.eu.apache.org/dist/tomcat/tomcat-connectors/jk/tomcat-connectors-1.2.41-src.tar.gz tar -xf tomcat-connectors-1.2.41-src.tar.gz
Compile and install mode_jk cd tomcat-connectors-1.2.41-src/native ./configure --with-apxs=/usr/bin/apxs make libtool --finish /usr/lib64/httpd/modules make install
Finally we need to install two more moduels for Apache (mod_rewrite and mod_proxy_html)
yum install mod_proxy_html mod_rewrite
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Prepare Apache for virtual hosts A virtual host is a web site controlled by a web server. The configuration of the virtual host is kept in a ”*.conf” file accessible by the web server program (on Redhat:”httpd” on Debian: ”apache2”). Typically these files are organized as one file for each site controlled by the web server and are located somewhere in the /etc/httpd folder (Debian: /etc/apache2).
A practal way to organize the files is to keep the actual *.conf files in a folder of available site and symlink to them from a folder of active sites (so the sites becomes active when there is a symlink and inactive when the symlink is removed) First create two folders in /etc/httpd folder cd /etc/httpd mkdir sites-available mkdir sites-enabled
Next make sure Apache sees the symlinked files by adding a line to the httpd.conf file nano conf/httpd.conf
Add this line to the end
IncludeOptional sites-enabled/*.conf save the file (ctrl+o,ctrl+x)
Setup the virtual host An important part of running a web site is to log errors and access. By default Apache writes all logs for all virtual hosts to the same files (usally in the folder /var/log/httpd or /var/log/apache)
To keep logs organized it may be better to keep the logs of each virtual host in separate files. In this case I will keep logs from the dbNP/GSCF file in a folder named gscf that I will create in the apache log folder
Create a folder ”gscf” in the apache log folder cd /var/log/httpd mkdir gscf The full path of this folder is ”/var/log/httpd/gscf”
Next I will create the file that defines the virtual host (it wil be called ”gscf.conf”) cd /etc/httpd nano sites-available/gscf.conf
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 18/24 PhenotypeDatabase / GSCF
The full content of the file (this is almost verbatim copy-paste from the PhenotypeDatabase github page)
# keep error and access logs in a separate dedicated folder # the folder must exist before trying to run this site ErrorLog /var/log/gscf/error_log CustomLog /var/log/gscf/access_log combined
# keep listening for the serveralias, but redirect to # servername instead to make sure only one user session # is created (tomcat will create one user session per # domain which may lead to two (or more) usersessions # depending on the number of serveraliases) # see gscf ticket #321 RewriteCond %{HTTP_HOST} ^test.gscf.mysite.com$ [NC] RewriteRule ^(.*)$ http://test.mysite.com$1 [R=301,L]
# rewrite the /gscf-a.b.c-environment/ part of the url RewriteCond %{HTTP_HOST} ^test.mysite.com$ [NC] RewriteRule ^/gscf/(.*)$ /$1 [L,PT,NC,NE]
ProxyStatus On ProxyPass / balancer://gscf-cluster/gscf/ stickysession=JSESSIONID|jsessionid nofailover=On ProxyPassReverse / balancer://gscf-cluster/gscf/ ProxyPassReverseCookiePath /gscf /
Save and restart apache (ctrl+0,ctrl+x)
systemctl restart httpd
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Installing dbNP/GSCF
As mentioned in the Tomcat setup section there are several ways to in install a webapp in Tomcat. In this section I am going to do a manual installation of the GSCF app. In the Tomcat folder is a subfolder named ”webapps” all the webapps controlled by Tomcat resides in this folder as subfolders (the PhenotypeDatabase webapp is going to be installed in a subfolder named ”gscf”)
First we need to download the latest version of the PhenotypeDatabase mkdir dbnp cd dbnp wget http://download.dbnp.org/production/PhenotypeDatabase.war
Next upzip the downloaded file directly to the tomcat webapps folder unzip PhenotypeDatabase.war -d /opt/tomcat/webapps/gscf
List the content of the gscf folder ls -l /opt/tomcat/webapps/gscf/ total 28 drwxr-xr-x 4 root root 4096 Mar 22 19:25 css drwxr-xr-x 2 root root 4096 Mar 22 19:25 downloads drwxr-xr-x 2 root root 6 Mar 22 19:25 fileuploads drwxr-xr-x 15 root root 4096 Mar 22 19:25 images drwxr-xr-x 7 root root 4096 Mar 22 19:25 js drwxr-xr-x 2 root root 24 Mar 22 19:25 META-INF drwxr-xr-x 11 root root 4096 Mar 22 19:25 plugins -rw-r--r-- 1 root root 233 Sep 8 2015 robots.txt drwxr-xr-x 9 root root 4096 Mar 22 19:25 WEB-INF drwxr-xr-x 2 root root 37 Mar 22 19:25 webtestfiles
Side note on other ways to install: Another way to do the install is to copy the original zipped war file to the tomcat/webapps folder, restart Tomcat and let Tomcat automatically unzip and install it. It appears that Tomcat will create a subfolder of the same name as the war-file, therefore if you choose this method you will need to rename the PhenotypeDatabase.war to gscf.war
The third way is to upload the file via the Manager App web interface – I have not tested this fully to a successful working installation.
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen Tutorial: Install dbNP on CentOS/RHEL 7 (v3) 20/24 PhenotypeDatabase / GSCF
Configuring dbNP/GSCF First create a subfolder ”.gscf” (note that it starts with a dot) in the tomcat folder cd /opt/tomcat mkdir .gscf
Next find the default example config file (webapps/gscf/WEB-INF/classes/default.properties) and copy it to ”.gscf”
cp webapps/gscf/WEB-INF/classes/default.properties .gscf
Edit the file (ctrl+o to save, ctrl+x to leave) nano .gscf/production.properties
I will go through this setup section for section
The default file
## Server URL ## grails.serverURL=http://localhost:8080/gscf
Server URL The server URL is used throughout this file, therefore it is better to create a variable to hold this value In this example the domain name is ”dashin-n04.vm” like this ipaddr=dashin-n04.vm This can then be used where needed like this
${ipaddr}
Consequently:
## Server URL ## ipaddr=dashin-n04.vm grails.serverURL=http://${ipaddr}:8080/gscf gscf.baseURL=http://${ipaddr}:8080/gscf
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The database disable the in-memory database, enable postgres default
… ## In-Memory Database ## dataSource.driverClassName=org.h2.Driver dataSource.url=jdbc:h2:mem:devDB dataSource.dbCreate=create-drop dataSource.username=sa dataSource.password=
## Database (disable in-memory database first) ## # dataSource.driverClassName=org.postgresql.Driver # dataSource.dialect=org.hibernate.dialect.PostgreSQLDialect # dataSource.url=jdbc:postgresql://localhost:5432/gscf-www # dataSource.dbCreate=update # dataSource.username=
My changes
... ## In-Memory Database ## #dataSource.driverClassName=org.h2.Driver #dataSource.url=jdbc:h2:mem:devDB #dataSource.dbCreate=create-drop #dataSource.username=sa #dataSource.password=
## Database (disable in-memory database first) ## dataSource.driverClassName=org.postgresql.Driver dataSource.dialect=org.hibernate.dialect.PostgreSQLDialect dataSource.url=jdbc:postgresql://localhost:5432/gscfwww dataSource.dbCreate=update dataSource.username=gscfuser dataSource.password=secret-pw ... Note: The database name (without dash)
Enable modules
... ## Module Configuration ## modules.showInMenu=true modules.sam.baseurl=http://localhost:8080/gscf/measurements/SAM modules.sam.url=gscf/measurements/SAM # modules.metabolomics.url=http://localhost:8083/metabolomicsModule # modules.massSequencing.url=http://localhost:8184/massSequencing ...
My changes
... ## Module Configuration ## modules.showInMenu=true modules.sam.baseurl=http://${ipaddr}:8080/gscf/measurements/SAM modules.sam.url=gscf/measurements/SAM modules.metabolomics.url=http://${ipaddr}:8083/metabolomicsModule modules.massSequencing.url=http://${ipaddr}:8184/massSequencing ...
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Default users These user will be written to the database during installation, so passwords can only be changed through the web interface.
... ## Default Application Users ## authentication.users.admin.username=admin authentication.users.admin.password=admiN123! [email protected] authentication.users.admin.administrator=true authentication.users.user.username=user authentication.users.user.password=useR123! [email protected] authentication.users.user.administrator=false ...
My changes
... ## Default Application Users ## authentication.users.admin.username=admin authentication.users.admin.password=adminpw [email protected] authentication.users.admin.administrator=true authentication.users.user.username=user authentication.users.user.password=userpw [email protected] authentication.users.user.administrator=false ...
API key From the PhenotypeDatabase site the API key must be obtained from the Bioportal organization at this address: https://bioportal.bioontology.org
Default
... ## Register and get your apikey here: https://bioportal.bioontology.org/account ## bioontology.resturl=http://data.bioontology.org/ bioontology.recommender=http://data.bioontology.org/recommender bioontology.apikey = your-apikey ...
My changes
... ## Register and get your apikey here: https://bioportal.bioontology.org/account ## bioontology.resturl=http://data.bioontology.org/ bioontology.recommender=http://data.bioontology.org/recommender bioontology.apikey = 518e253a-......
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Links to documents and downloads Default
... ## Locations of issues and documents ## gscf.issueURL=https://github.com/PhenotypeFoundation/PhenotypeDatabase/issues gscf.documents.quickguide=/interventionstudies/downloads/phenotype_database_quick_guide.pdf gscf.documents.study_manual=/interventionstudies/downloads/phenotype_database_study_manual.pdf gscf.documents.module_manual=/interventionstudies/downloads/phenotype_database_module_manual.pdf gscf.documents.license=/interventionstudies/downloads/phenotype_database_license_terms.pdf ...
My changes
… ## Locations of issues and documents ## gscf.issueURL=https://github.com/PhenotypeFoundation/PhenotypeDatabase/issues gscf.documents.quickguide=downloads/phenotype_database_quick_guide.pdf gscf.documents.study_manual=downloads/phenotype_database_study_manual.pdf gscf.documents.module_manual=downloads/phenotype_database_module_manual.pdf gscf.documents.license=downloads/phenotype_database_license_terms.pdf ...
Email setup Email turned out to be more complicated than expected. I didn't have a certificate on the server so the secure mail connection on port 465 did not work. I had to set it to port 25 (also other changes were needed)
Default
... ## Email configuration ## grails.mail.host=smtp.gmail.com grails.mail.port=465 [email protected] grails.mail.password=xxx [email protected] ... ## SpringSecurity E-Mail Settings ## grails.plugin.springsecurity.ui.register.emailFrom=registration@your.domain grails.plugin.springsecurity.ui.forgotPassword.emailFrom=forgot-password@your.domain grails.plugin.springsecurity.ui.forgotPassword.emailSubject="Phenotype Database Password Retrieval" ...
My changes
… ## Email configuration ## grails.mail.host=localhost grails.mail.port=25 grails.mail.username=user1 grails.mail.password=secret-pw [email protected] ... ## SpringSecurity E-Mail Settings ## grails.plugin.springsecurity.ui.register.emailFrom=registration@${ipaddr} grails.plugin.springsecurity.ui.forgotPassword.emailFrom=forgot-password@${ipaddr} grails.plugin.springsecurity.ui.forgotPassword.emailSubject="Phenotype Database Password Retrieval" ...
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Email setup (cont..) (This is probably only needed for insecure connection)
Create a new config file in the ”.gscf” folder cd /opt/tomcat nano .gscf/production.groovy
To find the original groovy config file go to the PhenotypeDatabase github page https://github.com/PhenotypeFoundation/PhenotypeDatabase
Browse to this file: grails-app/conf/Config.groovy
Look for this part (towards the end of the file) type (or copy) it into the production.groovy file
... // Mail plugin config, also see default.properties or your external config file grails { mail { disabled = false props = [ "mail.smtp.auth": "true", "mail.smtp.socketFactory.port": "465", "mail.smtp.socketFactory.class": "javax.net.ssl.SSLSocketFactory", "mail.smtp.socketFactory.fallback": "false" ] } }
...
Change it into this
// grails settings // Mail plugin config, also see default.properties or your external config file grails { mail { disabled = false props = [ "mail.smtp.auth": "true", "mail.smtp.socketFactory.port": "25", "mail.smtp.socketFactory.class": "javax.net.SocketFactory", "mail.smtp.socketFactory.fallback": "false" ] } }
Restart Tomcat – now everything should be ready to go systemctl restart tomcat
Vist your new dbNP site
Finn Sandø – Department of Nutrition, Exercise and Sports (NEXS) – University of Copenhagen