[galaxy-dev] Local Galaxy Apache Config

Hello Galaxy Admins,

I am attempting to setup a local production-grade Galaxy server for our department. Before I go ahead and "turn on" Galaxy for the first time, would you be so kind as to please review my Apache2 config files for errors? I want to be sure that things are in the correct place to save me from headaches down the road.

The overall goals of the configuration are: - always use HTTPS and secure FTP - make maximum use of the machine (multiple Apache processes, PostgreSQL, ProFTPD, etc.)

If it helps, Galaxy will be running on a: - Dell Precision T7500 - 2 x Intel Xeon X5690 @ 3.46 GHz - 96 GB RAM - Ubuntu 14.04 64-bit

Thank you for your help!

FYI: My config files are based on the instructions at https://wiki.galaxyproject.org/Admin/GetGalaxy and https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

############################## # # /etc/apache2/apache2.conf # ##############################

# Global configuration # # ServerRoot: The top of the directory tree under which the server's # configuration, error, and log files are kept. # # NOTE! If you intend to place this on an NFS (or otherwise network) # mounted filesystem then please read the Mutex documentation (available # at URL:http://httpd.apache.org/docs/2.4/mod/core.html#mutex); # you will save yourself a lot of trouble. # # Do NOT add a slash at the end of the directory path. # #ServerRoot "/etc/apache2"

# # The accept serialization lock file MUST BE STORED ON A LOCAL DISK. # Mutex file:${APACHE_LOCK_DIR} default

# # PidFile: The file in which the server should record its process # identification number when it starts. # This needs to be set in /etc/apache2/envvars # PidFile ${APACHE_PID_FILE}

# # Timeout: The number of seconds before receives and sends time out. # Timeout 300

# # KeepAlive: Whether or not to allow persistent connections (more than # one request per connection). Set to "Off" to deactivate. # KeepAlive On

# # MaxKeepAliveRequests: The maximum number of requests to allow # during a persistent connection. Set to 0 to allow an unlimited amount. # We recommend you leave this number high, for maximum performance. # MaxKeepAliveRequests 100

# # KeepAliveTimeout: Number of seconds to wait for the next request from the # same client on the same connection. # KeepAliveTimeout 5

# These need to be set in /etc/apache2/envvars User ${APACHE_RUN_USER} Group ${APACHE_RUN_GROUP}

# # HostnameLookups: Log the names of clients or just their IP addresses # e.g., www.apache.org (on) or 204.62.129.132 (off). # The default is off because it'd be overall better for the net if people # had to knowingly turn this feature on, since enabling it means that # each client request will result in AT LEAST one lookup request to the # nameserver. # HostnameLookups Off

# ErrorLog: The location of the error log file. # If you do not specify an ErrorLog directive within a <VirtualHost> # container, error messages relating to that virtual host will be # logged here. If you *do* define an error logfile for a <VirtualHost> # container, that host's errors will be logged there and not here. # ErrorLog ${APACHE_LOG_DIR}/error.log

# # LogLevel: Control the severity of messages logged to the error_log. # Available values: trace8, ..., trace1, debug, info, notice, warn, # error, crit, alert, emerg. # It is also possible to configure the log level for particular modules, e.g. # "LogLevel info ssl:warn" # LogLevel warn

# Include module configuration: IncludeOptional mods-enabled/*.load IncludeOptional mods-enabled/*.conf

# Include list of ports to listen on Include ports.conf

# Sets the default security model of the Apache2 HTTPD server. It does # not allow access to the root filesystem outside of /usr/share and /var/www. # The former is used by web applications packaged in Debian, # the latter may be used for local directories served by the web server. If # your system is serving content from a sub-directory in /srv you must allow # access here, or in any related virtual host. <Directory /> Options FollowSymLinks AllowOverride None Require all denied </Directory>

<Directory /usr/share> AllowOverride None Require all granted </Directory>

<Directory /var/www/> Options Indexes FollowSymLinks AllowOverride None Require all granted </Directory>

#<Directory /srv/> # Options Indexes FollowSymLinks # AllowOverride None # Require all granted #</Directory>

# AccessFileName: The name of the file to look for in each directory # for additional configuration directives. See also the AllowOverride # directive. # AccessFileName .htaccess

# # The following lines prevent .htaccess and .htpasswd files from being # viewed by Web clients. # <FilesMatch "^.ht"> Require all denied </FilesMatch>

# # The following directives define some format nicknames for use with # a CustomLog directive. # # These deviate from the Common Log Format definitions in that they use %O # (the actual bytes sent including headers) instead of %b (the size of the # requested file), because the latter makes it impossible to detect partial # requests. # # Note that the use of %{X-Forwarded-For}i instead of %h is not recommended. # Use mod_remoteip instead. # LogFormat "%v:%p %h %l %u %t "%r" %>s %O "%{Referer}i" "%{User-Agent}i"" vhost_combined LogFormat "%h %l %u %t "%r" %>s %O "%{Referer}i" "%{User-Agent}i"" combined LogFormat "%h %l %u %t "%r" %>s %O" common LogFormat "%{Referer}i -> %U" referer LogFormat "%{User-agent}i" agent

# Include of directories ignores editors' and dpkg's backup files, # see README.Debian for details.

<Location "/"> # Makes galaxy aware of what type of URL it should generate for external sites like Biomart. RequestHeader set X-URL-SCHEME https # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI .(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI .(?:t?gz|zip|bz2)$ no-gzip dont-vary SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary # This speeds up downloads. XSendFile on XSendFilePath / </Location> <Location "/static"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" </Location>

# Include generic snippets of statements IncludeOptional conf-enabled/*.conf

# Include the virtual host configurations: IncludeOptional sites-enabled/*.conf

# vim: syntax=apache ts=4 sw=4 sts=4 sr noet

############################## # # /etc/apache2/sites-available/000-default.conf # ##############################

<VirtualHost *:80> # The ServerName directive sets the request scheme, hostname and port that # the server uses to identify itself. This is used when creating # redirection URLs. In the context of virtual hosts, the ServerName # specifies what hostname must appear in the request's Host: header to # match this virtual host. For the default virtual host (this file) this # value is not decisive as it is used as a last resort host regardless. # However, you must set it for any further virtual host explicitly.

ServerName computer.school.edu ServerAdmin awesome.admin@school.edu DocumentRoot /var/www/html

# Available loglevels: trace8, ..., trace1, debug, info, notice, warn, # error, crit, alert, emerg. # It is also possible to configure the loglevel for particular # modules, e.g. #LogLevel info ssl:warn

ErrorLog ${APACHE_LOG_DIR}/error.log CustomLog ${APACHE_LOG_DIR}/access.log combined

# For most configuration files from conf-available/, which are # enabled or disabled at a global level, it is possible to # include a line for only one particular virtual host. For example the # following line enables the CGI configuration for this host only # after it has been globally disabled with "a2disconf". #Include conf-available/serve-cgi-bin.conf

# Allow display sites such as UCSC. <Location "/root/display_as"> Satisfy Any Order deny,allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location>

#<Proxy balancer://galaxy> # BalancerMember http://localhost:8400 # BalancerMember http://localhost:8401 #</Proxy>

<Proxy balancer://galaxy> BalancerMember http://localhost:8080 BalancerMember http://localhost:8081 BalancerMember http://localhost:8082 BalancerMember http://localhost:8083 BalancerMember http://localhost:8084 BalancerMember http://localhost:8085 BalancerMember http://localhost:8086 BalancerMember http://localhost:8087 BalancerMember http://localhost:8088 BalancerMember http://localhost:8089 </Proxy>

# Proxy requests to the Galaxy application. RewriteEngine on RewriteRule ^/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] # This line: #RewriteRule ^(.*) http://localhost:8080$1 [P] # ...replaced with this line: RewriteRule ^(.*) balancer://galaxy$1 [P] </VirtualHost>

# vim: syntax=apache ts=4 sw=4 sts=4 sr noet

############################## # # /etc/apache2/sites-available/default-ssl.conf # ##############################

<IfModule mod_ssl.c> <VirtualHost _default_:443>

ServerAdmin awesome.admin@school.edu DocumentRoot /var/www/html

# Available loglevels: trace8, ..., trace1, debug, info, notice, warn, # error, crit, alert, emerg. # It is also possible to configure the loglevel for particular # modules, e.g. #LogLevel info ssl:warn

ErrorLog ${APACHE_LOG_DIR}/error.log CustomLog ${APACHE_LOG_DIR}/access.log combined

# For most configuration files from conf-available/, which are # enabled or disabled at a global level, it is possible to # include a line for only one particular virtual host. For example the # following line enables the CGI configuration for this host only # after it has been globally disabled with "a2disconf". #Include conf-available/serve-cgi-bin.conf

# SSL Engine Switch: # Enable/Disable SSL for this virtual host. SSLEngine on

# A self-signed (snakeoil) certificate can be created by installing # the ssl-cert package. See # /usr/share/doc/apache2/README.Debian.gz for more info. # If both key and certificate are stored in the same file, only the # SSLCertificateFile directive is needed. #SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem #SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key SSLCertificateFile /etc/ssl/certs/server.crt SSLCertificateKeyFile /etc/ssl/private/server.key

# Server Certificate Chain: # Point SSLCertificateChainFile at a file containing the # concatenation of PEM encoded CA certificates which form the # certificate chain for the server certificate. Alternatively # the referenced file can be the same as SSLCertificateFile # when the CA certificates are directly appended to the server # certificate for convinience. #SSLCertificateChainFile /etc/apache2/ssl.crt/server-ca.crt

# Certificate Authority (CA): # Set the CA certificate verification path where to find CA # certificates for client authentication or alternatively one # huge file containing all of them (file must be PEM encoded) # Note: Inside SSLCACertificatePath you need hash symlinks # to point to the certificate files. Use the provided # Makefile to update the hash symlinks after changes. #SSLCACertificatePath /etc/ssl/certs/ #SSLCACertificateFile /etc/apache2/ssl.crt/ca-bundle.crt

# Certificate Revocation Lists (CRL): # Set the CA revocation path where to find CA CRLs for client # authentication or alternatively one huge file containing all # of them (file must be PEM encoded) # Note: Inside SSLCARevocationPath you need hash symlinks # to point to the certificate files. Use the provided # Makefile to update the hash symlinks after changes. #SSLCARevocationPath /etc/apache2/ssl.crl/ #SSLCARevocationFile /etc/apache2/ssl.crl/ca-bundle.crl

# Client Authentication (Type): # Client certificate verification type and depth. Types are # none, optional, require and optional_no_ca. Depth is a # number which specifies how deeply to verify the certificate # issuer chain before deciding the certificate is not valid. #SSLVerifyClient require #SSLVerifyDepth 10

# SSL Engine Options: # Set various options for the SSL engine. # o FakeBasicAuth: # Translate the client X.509 into a Basic Authorisation. This means that # the standard Auth/DBMAuth methods can be used for access control. The # user name is the `one line' version of the client's X.509 certificate. # Note that no password is obtained from the user. Every entry in the user # file needs this password: `xxj31ZMTZzkVA'. # o ExportCertData: # This exports two additional environment variables: SSL_CLIENT_CERT and # SSL_SERVER_CERT. These contain the PEM-encoded certificates of the # server (always existing) and the client (only existing when client # authentication is used). This can be used to import the certificates # into CGI scripts. # o StdEnvVars: # This exports the standard SSL/TLS related `SSL_*' environment variables. # Per default this exportation is switched off for performance reasons, # because the extraction step is an expensive operation and is usually # useless for serving static content. So one usually enables the # exportation for CGI and SSI requests only. # o OptRenegotiate: # This enables optimized SSL connection renegotiation handling when SSL # directives are used in per-directory context. #SSLOptions +FakeBasicAuth +ExportCertData +StrictRequire <FilesMatch ".(cgi|shtml|phtml|php)$"> SSLOptions +StdEnvVars </FilesMatch> <Directory /usr/lib/cgi-bin> SSLOptions +StdEnvVars </Directory>

# SSL Protocol Adjustments: # The safe and default but still SSL/TLS standard compliant shutdown # approach is that mod_ssl sends the close notify alert but doesn't wait for # the close notify alert from client. When you need a different shutdown # approach you can use one of the following variables: # o ssl-unclean-shutdown: # This forces an unclean shutdown when the connection is closed, i.e. no # SSL close notify alert is send or allowed to received. This violates # the SSL/TLS standard but is needed for some brain-dead browsers. Use # this when you receive I/O errors because of the standard approach where # mod_ssl sends the close notify alert. # o ssl-accurate-shutdown: # This forces an accurate shutdown when the connection is closed, i.e. a # SSL close notify alert is send and mod_ssl waits for the close notify # alert of the client. This is 100% SSL/TLS standard compliant, but in # practice often causes hanging connections with brain-dead browsers. Use # this only for browsers where you know that their SSL implementation # works correctly. # Notice: Most problems of broken clients are also related to the HTTP # keep-alive facility, so you usually additionally want to disable # keep-alive for those clients, too. Use variable "nokeepalive" for this. # Similarly, one has to force some clients to use HTTP/1.0 to workaround # their broken HTTP/1.1 implementation. Use variables "downgrade-1.0" and # "force-response-1.0" for this. BrowserMatch "MSIE [2-6]" \ nokeepalive ssl-unclean-shutdown \ downgrade-1.0 force-response-1.0 # MSIE 7 and newer should be able to use keepalive BrowserMatch "MSIE [17-9]" ssl-unclean-shutdown

</VirtualHost> </IfModule>

# vim: syntax=apache ts=4 sw=4 sts=4 sr noet