https://github.com/genome/genome
Tip revision: 1260120b5b1b9cc4c25e9e5e4c35c6e628ee0508 authored by Chris Miller on 28 August 2013, 21:59:26 UTC
revamped tool to work on newer file formats instead of just using Varscan input
revamped tool to work on newer file formats instead of just using Varscan input
Tip revision: 1260120
imp.gsc.wustl.edu-ssl.conf
<VirtualHost *:80>
ServerName imp.gsc.wustl.edu
ServerAlias imp
RewriteEngine On
RewriteCond %{REQUEST_URI} !^/server-status
RewriteRule /(.*) https://imp.gsc.wustl.edu/$1 [R=permanent,L]
</VirtualHost>
<IfModule mod_ssl.c>
##
## SSL Virtual Host Context
##
<VirtualHost *:443>
ServerAdmin webmaster@gsc.wustl.edu
ServerName imp.gsc.wustl.edu
ServerAlias imp
# SuexecUserGroup: Sets the domain to run as a specific user when
# executing processes.
# SuexecUserGroup USER GROUP
Include /opt/shibboleth-sp/etc/shibboleth/apache22.config
<Location />
Allow from all
AuthType shibboleth
ShibRequireSession On
Require valid-user
</Location>
<Location />
Order allow,deny
Allow from 10.0.24.51
Allow from 10.0.28.107
AuthType shibboleth
ShibRequireSession On
Require valid-user
Satisfy Any
</Location>
<Location /static>
Allow from all
Satisfy Any
</Location>
# DocumentRoot: The directory out of which you will serve your
# documents. By default, all requests are taken from this directory, but
# symbolic links and aliases may be used to point to other locations.
DocumentRoot /var/www/domains/gsc.wustl.edu/imp/htdocs
Alias /resources /gsc/scripts/opt/genome/current/web/lib/perl/Genome/View/Resource/Html/old
Alias /var/ /gsc/var/
<Directory /gsc/var>
Options Indexes MultiViews FollowSymLinks
Order deny,allow
Deny from all
Allow from 10
</Directory>
# if not specified, the global error log is used
# If logging to standard access and error logs comment the cronlog line and uncomment below
#ErrorLog /var/www/domains/gsc.wustl.edu/imp/logs/error_log
#CustomLog /var/www/domains/gsc.wustl.edu/imp/logs/access_log combined
# Default logging is now Cronolog, please make sure cronolog is installed before restarting Apache.
ErrorLog "|/usr/bin/cronolog -l /var/www/domains/gsc.wustl.edu/imp/logs/error_log /var/www/domains/gsc.wustl.edu/imp/logs/%Y/%Y-%m-error_log"
CustomLog "|/usr/bin/cronolog -l /var/www/domains/gsc.wustl.edu/imp/logs/access_log /var/www/domains/gsc.wustl.edu/imp/logs/%Y/%Y-%m-access_log" combined
# Do not lose time with IP address lookups
HostnameLookups Off
# Needed for named virtual hosts
UseCanonicalName Off
# Configures the footer on server-generated documents
ServerSignature Off
ScriptAlias /cgi-bin "/var/www/domains/gsc.wustl.edu/imp/cgi-bin"
# ScriptAlias /view/ "/gsc/scripts/lib/perl/Genome/Model/Command/Services/WebApp/Main.psgi/view/"
# ScriptAlias /search "/var/www/domains/gsc.wustl.edu/imp/cgi-bin/search/index.cgi"
# ScriptAlias /res/ "/gsc/scripts/lib/perl/Genome/Model/Command/Services/WebApp/Main.psgi/res/"
# Alias /res "/gsc/scripts/opt/genome-webapp/lib/perl/Genome/View/Resource/Html/"
# Alias /view/genome/resource.html "/gsc/scripts/opt/genome-webapp/lib/perl/Genome/View/Resource/Html/"
Alias /res "/gsc/scripts/opt/genome/current/web/lib/perl/Genome/View/Resource/Html/"
Alias /view/genome/resource.html "/gsc/scripts/opt/genome/current/web/lib/perl/Genome/View/Resource/Html/"
FastCgiExternalServer /tmp/genome.fcgi -host apipe.gsc.wustl.edu:3060 -idle-timeout 600
# Alias /view /tmp/genome.fcgi/view
# Alias /viewajax /tmp/genome.fcgi/viewajax
## to disable view memcache, comment out these 3 lines and uncomment the above two
Alias /cachetrigger /tmp/genome.fcgi/cachetrigger
Alias /viewajax /tmp/genome.fcgi/cachefill
Alias /view /tmp/genome.fcgi/cache
RewriteEngine On
RewriteRule ^/search/$ /search [PT]
Alias /search /tmp/genome.fcgi/view/genome/search/status.html
RewriteCond %{HTTP_USER_AGENT} ^curl.*
RewriteRule ^/cachetrigger.*$ - [F]
# FastCgiExternalServer /tmp/myapp.fcgi -host localhost:3010 -idle-timeout 3600
# Alias / /tmp/myapp.fcgi/
FastCgiExternalServer /tmp/myapp.fcgi -host lims-fcgi.gsc.wustl.edu:3010 -idle-timeout 3600
Alias / /tmp/myapp.fcgi/
<Directory "/var/www/domains/gsc.wustl.edu/imp/cgi-bin">
AllowOverride None
Options ExecCGI -MultiViews +SymLinksIfOwnerMatch
Order allow,deny
Allow from all
</Directory>
<Directory /var/www/domains/gsc.wustl.edu/imp/htdocs>
Options -Indexes ExecCGI FollowSymLinks
AllowOverride All
</Directory>
# SSL Engine Switch:
# Enable/Disable SSL for this virtual host.
SSLEngine on
# SSL Cipher Suite:
# List the ciphers that the client is permitted to negotiate.
# See the mod_ssl documentation for a complete list.
# to display accepted from a shell use: openssl ciphers -v 'HIGH:+MEDIUM'
#SSLCipherSuite ALL:!ADH:!EXPORT56:RC4+RSA:+HIGH:+MEDIUM:+LOW:+SSLv2:+EXP:+eNULL
SSLCipherSuite HIGH:+MEDIUM
# Server Certificate:
# Point SSLCertificateFile at a PEM encoded certificate. If
# the certificate is encrypted, then you will be prompted for a
# pass phrase. Note that a kill -HUP will prompt again. Keep
# in mind that if you have both an RSA and a DSA certificate you
# can configure both in parallel (to also allow the use of DSA
# ciphers, etc.)
#SSLCertificateFile /etc/httpd/conf/ssl.crt/server.crt
#SSLCertificateFile /etc/httpd/conf/ssl.crt/server-dsa.crt
SSLCertificateFile /var/www/domains/gsc.wustl.edu/imp/ssl/imp.gsc.wustl.edu.crt
# Server Private Key:
# If the key is not combined with the certificate, use this
# directive to point at the key file. Keep in mind that if
# you've both a RSA and a DSA private key you can configure
# both in parallel (to also allow the use of DSA ciphers, etc.)
#SSLCertificateKeyFile /etc/httpd/conf/ssl.key/server.key
#SSLCertificateKeyFile /etc/httpd/conf/ssl.key/server-dsa.key
SSLCertificateKeyFile /var/www/domains/gsc.wustl.edu/imp/ssl/imp.gsc.wustl.edu.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.
#SSLCertificateFile /etc/httpd/conf/ssl.crt/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/httpd/conf/ssl.crt
#SSLCACertificateFile /etc/httpd/conf/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/httpd/conf/ssl.crl
#SSLCARevocationFile /etc/httpd/conf/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
# Access Control:
# With SSLRequire you can do per-directory access control based
# on arbitrary complex boolean expressions containing server
# variable checks and other lookup directives. The syntax is a
# mixture between C and Perl. See the mod_ssl documentation
# for more details.
#<Location />
#SSLRequire ( %{SSL_CIPHER} !~ m/^(EXP|NULL)/ \
# and %{SSL_CLIENT_S_DN_O} eq "Snake Oil, Ltd." \
# and %{SSL_CLIENT_S_DN_OU} in {"Staff", "CA", "Dev"} \
# and %{TIME_WDAY} >= 1 and %{TIME_WDAY} <= 5 \
# and %{TIME_HOUR} >= 8 and %{TIME_HOUR} <= 20 ) \
# or %{REMOTE_ADDR} =~ m/^192\.76\.162\.[0-9]+$/
#</Location>
# SSL Engine Options:
# Set various options for the SSL engine.
# o FakeBasicAuth:
# Translate the client X.509 into a Basic Authorisation. This means that
# the standard Auth/DBMAuth methods can be used for access control. The
# user name is the `one line' version of the client's X.509 certificate.
# Note that no password is obtained from the user. Every entry in the user
# file needs this password: `xxj31ZMTZzkVA'.
# o ExportCertData:
# This exports two additional environment variables: SSL_CLIENT_CERT and
# SSL_SERVER_CERT. These contain the PEM-encoded certificates of the
# server (always existing) and the client (only existing when client
# authentication is used). This can be used to import the certificates
# into CGI scripts.
# o StdEnvVars:
# This exports the standard SSL/TLS related `SSL_*' environment variables.
# Per default this exportation is switched off for performance reasons,
# because the extraction step is an expensive operation and is usually
# useless for serving static content. So one usually enables the
# exportation for CGI and SSI requests only.
# o CompatEnvVars:
# This exports obsolete environment variables for backward compatibility
# to Apache-SSL 1.x, mod_ssl 2.0.x, Sioux 1.0 and Stronghold 2.x. Use this
# to provide compatibility to existing CGI scripts.
# o StrictRequire:
# This denies access when "SSLRequireSSL" or "SSLRequire" applied even
# under a "Satisfy any" situation, i.e. when it applies access is denied
# and no other module can change it.
# o OptRenegotiate:
# This enables optimized SSL connection renegotiation handling when SSL
# directives are used in per-directory context.
#SSLOptions +FakeBasicAuth +ExportCertData +CompatEnvVars +StrictRequire
#<Files ~ "\.(cgi|shtml|phtml|php3?)$">
# SSLOptions +StdEnvVars
#</Files>
#<Directory "/srv/www/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.
SetEnvIf User-Agent ".*MSIE.*" \
nokeepalive ssl-unclean-shutdown \
downgrade-1.0 force-response-1.0
# Per-Server Logging:
# The home of a custom SSL log file. Use this when you want a
# compact non-error SSL logfile on a virtual host basis.
CustomLog /var/www/domains/gsc.wustl.edu/imp/logs/ssl_request_log ssl_combined
</VirtualHost>
</IfModule>