version v1.5

README.md

@@ -1,23 +1,22 @@
 # EDGE Bioinformatics
 
-This is version 1.1.1 of EDGE Bioinformatics, a product of Los Alamos National Laboratory, Naval Medical Research Center, and the Defense Threat Reduction Agency.
+This is version 1.5 of EDGE Bioinformatics, a product of Los Alamos National Laboratory, Naval Medical Research Center, and the Defense Threat Reduction Agency.
 
 EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data. The bioinformatics platform allows users to address a wide range of use cases including assay validation and the characterization of novel biological threats, clinical samples, and complex environmental samples.
 
-A demonstration version of EDGE is currently available at https://bioedge.lanl.gov/edge_ui/ with example data sets available to the public to view and/or re-run and also allows EDGE runs of SRA/ENA data. (This webserver does not currently support upload of data due in part to LANL security regulations, however local installations are meant to be fully functional.) To run EDGE follow the "GUI" instructions from our documentation, found at https://edge.readthedocs.org/en/v1.1/introduction.html. It is also linked at the bottom of the EDGE homepage.
-
-For basic information about EDGE, visit the <a href="https://edge.readthedocs.io/en/latest/EDGE_ABCs.html" >EDGE ABC's</a>, that provide a brief overview of EDGE, the various workflows, and the computational environment restraints for local use.
+To demo EDGE, go to https://bioedge.lanl.gov/edge_ui/ and follow the "GUI" instructions from our documentation, found at https://edge.readthedocs.io. It is also linked at the bottom of the EDGE homepage.
 
 ## Documentation
 
-[ReadTheDocs](http://edge.readthedocs.org)
+[ReadTheDocs](http://edge.readthedocs.io)
 
-[PDF](https://readthedocs.org/projects/edge/downloads/pdf/latest/)
+[PDF](https://media.readthedocs.org/pdf/edge/v1.5/edge.pdf)
 
 ## Contact Info
 Chien-Chi Lo: <[email protected]>  
 Paul Li: <[email protected]>  
-Joe Anderson (DTRA/NMRC): <[email protected]> 
+Joe Anderson (DTRA/NMRC): <[email protected]>
+Logan Voegtly (HJF/NMRC): <[email protected]>
 
 ## Citation
 

config_template.txt

@@ -52,11 +52,16 @@ nanoporeFile=
 [Reads Mapping To Contigs]
 # Reads mapping to contigs
 DoReadsMappingContigs=auto
+## support bowtie or bwa
+edge-r2c-aligner=bowtie
+edge-r2c-aligner-options=
 
 [Reads Mapping To Reference]
 # Reads mapping to reference
-DoReadsMappingReference=0
-bowtieOptions=
+DoReadsMappingReference=
+## support bowtie or bwa
+edge-r2g-aligner=bowtie
+edge-r2g-aligner-options=
 # reference genbank or fasta file
 reference=
 MapUnmappedReads=0
@@ -66,7 +71,7 @@ MapUnmappedReads=0
 DoReadsTaxonomy=1
 ## If reference genome exists, only use unmapped reads to do Taxonomy Classification. Turn on AllReads=1 will use all reads instead.
 AllReads=0
-enabledTools=gottcha-genDB-b,gottcha-speDB-b,gottcha-strDB-b,gottcha-genDB-v,gottcha-speDB-v,gottcha-strDB-v,metaphlan,bwa,kraken_mini
+enabledTools=gottcha-genDB-b,gottcha-speDB-b,gottcha-strDB-b,gottcha-genDB-v,gottcha-speDB-v,gottcha-strDB-v,metaphlan,bwa,kraken_mini,metascope
 
 [Contigs Mapping To Reference]
 # Contig mapping to reference
@@ -99,15 +104,15 @@ annotateSourceGBK=
 [ProPhage Detection]
 DoProPhageDetection=1
 
-[SNP Phylogeny]
+[Phylogenetic Analysis]
 DoSNPtree=1
 ## Availabe choices are Ecoli, Yersinia, Francisella, Brucella, Bacillus
 SNPdbName=Ecoli
 ## List of genome name from NCBI genomes see $EDGE/edge_ui/data/Ref_list.json
 SNPGenomes=
 SNPGenomesFiles=
 ## A refrence genoem from above two options for reads/contigs mapping
-SNPrefGenome=<TMPL_VAR NAME=edge-phylo-ref-select-ref>
+SNPrefGenome=
 ## FastTree or RAxML
 treeMaker=FastTree
 ## SRA accessions ByrRun, ByExp, BySample, ByStudy

deployment/apache2.conf

@@ -0,0 +1,284 @@
+# This is the main Apache server configuration file.  It contains the
+# configuration directives that give the server its instructions.
+# See http://httpd.apache.org/docs/2.4/ for detailed information about
+# the directives and /usr/share/doc/apache2/README.Debian about Debian specific
+# hints.
+#
+#
+# Summary of how the Apache 2 configuration works in Debian:
+# The Apache 2 web server configuration in Debian is quite different to
+# upstream's suggested way to configure the web server. This is because Debian's
+# default Apache2 installation attempts to make adding and removing modules,
+# virtual hosts, and extra configuration directives as flexible as possible, in
+# order to make automating the changes and administering the server as easy as
+# possible.
+
+# It is split into several files forming the configuration hierarchy outlined
+# below, all located in the /etc/apache2/ directory:
+#
+#	/etc/apache2/
+#	|-- apache2.conf
+#	|	`--  ports.conf
+#	|-- mods-enabled
+#	|	|-- *.load
+#	|	`-- *.conf
+#	|-- conf-enabled
+#	|	`-- *.conf
+# 	`-- sites-enabled
+#	 	`-- *.conf
+#
+#
+# * apache2.conf is the main configuration file (this file). It puts the pieces
+#   together by including all remaining configuration files when starting up the
+#   web server.
+#
+# * ports.conf is always included from the main configuration file. It is
+#   supposed to determine listening ports for incoming connections which can be
+#   customized anytime.
+#
+# * Configuration files in the mods-enabled/, conf-enabled/ and sites-enabled/
+#   directories contain particular configuration snippets which manage modules,
+#   global configuration fragments, or virtual host configurations,
+#   respectively.
+#
+#   They are activated by symlinking available configuration files from their
+#   respective *-available/ counterparts. These should be managed by using our
+#   helpers a2enmod/a2dismod, a2ensite/a2dissite and a2enconf/a2disconf. See
+#   their respective man pages for detailed information.
+#
+# * The binary is called apache2. Due to the use of environment variables, in
+#   the default configuration, apache2 needs to be started/stopped with
+#   /etc/init.d/apache2 or apache2ctl. Calling /usr/bin/apache2 directly will not
+#   work with the default configuration.
+
+
+# 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>
+
+    Alias / "/home/edge/edge/edge_ui/"
+    <Directory "/home/edge/edge/edge_ui">
+        Options Indexes FollowSymlinks
+        AllowOverride None
+        Require all granted
+    </Directory>
+
+
+    ScriptAlias /cgi-bin/ /home/edge/edge/edge_ui/cgi-bin/
+    <Directory "/home/edge/edge/edge_ui/cgi-bin">
+        AllowOverride None
+        Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
+        AddHandler cgi-script .cgi .pl
+        Order allow,deny
+        allow from all
+    </Directory>
+
+#for JBrowse
+AddType application/octet-stream .bam .bami
+
+<IfModule mod_gzip.c>
+    mod_gzip_item_exclude "(\.jsonz|\.txtz)"
+</IfModule>
+<IfModule setenvif.c>
+    SetEnvIf Request_URI "(\.jsonz|\.txtz)" no-gzip dont-vary
+</IfModule>
+<IfModule mod_headers.c>
+	<FilesMatch "(\.jsonz|\.txtz)">
+		Header onsuccess set Content-Encoding gzip
+	</FilesMatch>
+</IfModule>
+
+<Directory /var/www/JBrowse/>
+  AllowOverride FileInfo
+</Directory>
+
+<IfModule mod_alias.c>
+	ScriptAlias /edge_ui/cgi-bin/ /home/edge/edge/edge_ui/cgi-bin/
+	<Directory "/home/edge/edge/edge_ui/cgi-bin">
+		AllowOverride None
+		Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
+		AddHandler cgi-script .cgi .pl
+		Order allow,deny
+		allow from all
+	</Directory>
+</IfModule>
+
+<IfModule alias_module>
+	Alias /edge_ui/ "/home/edge/edge/edge_ui/"
+	<Directory "/home/edge/edge/edge_ui">
+		Options Indexes FollowSymlinks
+		AllowOverride None
+		Require all granted
+	</Directory>
+</IfModule>
+
+<Directory /home/edge/edge/edge_ui/*/>
+        Options -Indexes
+</Directory>
+
+<Directory /var/www/edge_ui/>
+  Order allow,deny
+  Allow from all
+</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.
+
+# 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

deployment/createDatabase.sql

@@ -0,0 +1,5 @@
+CREATE DATABASE IF NOT EXIST userManagement;
+LOAD ~/edge/userManagement/userManagement_schema.sql;
+LOAD ~/edge/userManagement/userManagement_constrains.sql;
+CREATE USER 'edge'@'localhost' IDENTIFIED BY 'changePassword';
+GRANT ALL PRIVILEGES ON userManagement.* TO 'edge'@'localhost';