tropix.config.dir=${user.home}/.tropix
tropix.shortname.config.dir=${tropix.config.dir}/shortname

tomcat -Dtropix.config.dir=C:\etc


tropix.client.config.dir - 

authenticationSources.xml - Used to define potential login mechanisms. The following 
example demonstrates the xml format used.

<authenticationSources xmlns="http://msi.umn.edu/tropix/client/authentication/config">
  <caGrid title="MSI Ldap"
          authenticationServiceUrl="https://cagrid-authentication.msi.umn.edu:8443/wsrf/services/cagrid/AuthenticationService"
          dorianServiceUrl="https://cagrid-dorian.msi.umn.edu:8443/wsrf/services/cagrid/Dorian" />
  <local />
</authenticationSources>

This defines two login mechanisms, one that uses a caGrid
authentication and dorian service titled "MSI Ldap" and another that
just uses a local authentication mechanism that comes packaged with
Tint by default. Multiple caGrid entries may appear inside the
authenticationSources tag, and 0 or 1 local tags. These options will
be presented to the user in the order they appear in this XML file.

directory-services.properties - This file defines Tropix directory serivces to use if person.source=directoryService.
Entries in this file should be of the form

INSTITUTION_NAME=DIRECTORY_SERVICE_URL

Whitespace in INSTITUTION_NAME must be escaped with a backslash. Here is an example of this file that we use at MSI:

MSI=https://tropix-services.msi.umn.edu:8443/wsrf/services/cagrid/TropixDirectoryService
Mayo=https://tropix.mayo.edu:8443/wsrf/services/cagrid/TropixDirectoryService

catalog-services.properties - This file defines a list of catalog services along with their corresponding request service.
This file must be present if the CATALOG module is loaded. 

Here is an example that we use the MSI, notice how colons are escaped in the catalog service url.

http\://chilton.msi.umn.edu\:8090/wsrf/services/cagrid/TropixCatalogService=https://chilton.msi.umn.edu:8442/wsrf/services/cagrid/TropixRequestService
https\://tropix.mayo.edu\:8443/wsrf/services/cagrid/TropixCatalogService=https://tropix.mayo.edu:8443/wsrf/services/cagrid/TropixRequestService

deploy.properties file

# Required if person.source=directorySource or if Request module is loaded.
# A host credential consists of two files a cert file and a key file. The following
# two settings should be paths to these files
host.credential.cert=
host.credential.proxy= 

# person.soruce can be set to local or directoryService. If local is set, the user list
# used for sharing files is generated from the metadata database. If directoryService is
# the value, the file ${tropix.client.config.dir}/authentication-services.properties is 
# used to define directory services that are used to populate this list, and a host credential
# must be defined via host.credential.prefix to poll these services.
person.source=local

# Lifetime of generated user proxies (in seconds)
proxy.lifetime=43200

# Amount of time a user session lasts (in seconds)
login.timeout=43200

# Lifetime of delegated credential
delegated.credential.lifetime=300

# Credential delegatation service to use. Credential delegation is not preformed if this 
# is not specified. The training grid CredentialDelegationService is
# https://cds.training.cagrid.org:8443/wsrf/services/cagrid/CredentialDelegationService
cds.service.url= 

# Comma seperated list of grid identities that may resolve delegated credentials
cds.allowed.parties= 

# caGrid index service used to obtain dynamic service lists.
index.service.url=http://index.training.cagrid.org:8080/wsrf/services/DefaultIndexService

# Comma separated list of extra services to use.
unindexed.service.urls=

# Comma separated list of services that should not be used
blocked.service.urls=

# URL of the web container that contains the catalog instance to be
# writable by this GUI if the CATALOG module is loaded. Catlaog web service APIs
# will be loaded relative to this url, for instance of local.catalog.host=http://yahoo.com/
# the Catalog Ontology API is assumed to be at http://yahoo.com/CatalogAPI/services/CatalogOntAPISOAP
local.catalog.host=http://localhost:8080/

# Required if storage.type=cagrid, it is the url of the default storage
# service url to use.
storage.service.url=

# Required if the REQUEST module is loaded.
request.service.url=

# Comma separated list chosen from the following: SHARING, PROTIP, GENETIP, LOCAL_SEARCH, REQUEST, CATALOG, GRID_SEARCH
modules=SHARING, LOCAL_SEARCH

metadata.db.url
metadata.db.driver
metadata.db.username
metadata.db.password
metadata.db.dialect
metadata.db.hbm2ddl
metadata.db.showsql

# Can be local or cagrid
storage.type=local

# Port for embedded Jetty container to handle file transfer if storage.type=lcaol
httptransfer.server.port=13139

# The local storage mechanism needs your hostname or ip address. Java generally 
# can determine this but may get it wrong. If this occurs, it can be manually specified
# via this property.
hostname=

# If storage.type=local the storage.directory property specifies where
# to store saved files.
storage.directory=${tropix.storage.config.dir}/files

# The properties storage.candelete.ids, storage.canread.ids,
# storage.canwrite.ids can also be specified but these are really
# only useful in the standalone storage service deployment scenerio.

jobclient.db.url
jobclient.db.driver
jobclient.db.username
jobclient.db.password
jobclient.db.dialect
jobclient.db.hbm2ddl
jobclient.db.showsql

localauthentication.db.url
localauthentication.db.driver
localauthentication.db.username
localauthentication.db.password
localauthentication.db.dialect
localauthentication.db.hbm2ddl
localauthentication.db.showsql

requestaction.db.url
requestaction.db.driver
requestaction.db.username
requestaction.db.password
requestaction.db.dialect
requestaction.db.hbm2ddl
requestaction.db.showsql

Database properties shortname.db.*

# JDBC Url of database to use for this component.
shortname.db.url=jdbc:h2:${tropix.shortname.config.dir}/db

# Username and password for database
shortname.db.username=sa
shortname.db.password=

shortname.db.driver=


Common for all analytic services - 

# Name of the service, defaults to "Sequest", "XTandem", etc...
service.name=
# Description of the service
service.description=
# Path to an XML file describing the research center the service is hosted
# at as defined in the caGrid service metadata type. An outline of this file
# is as follows
# <ResearchCenter displayName="" shortName="" xmlns="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.common">
#   <Address country="" locality="" postalCode="" stateProvince="" street1="" street2=""/>
#   <pointOfContactCollection>
#     <PointOfContact affiliation="" email="" firstName="" lastName="" phoneNumber="" role=""/>
#   </pointOfContactCollection>
# </ResearchCenter>
service.researchcenter.path=

# Comma seperated list of caGrid index services to advertise with
advertise.index.service.urls=http://index.training.cagrid.org:8080/wsrf/services/DefaultIndexService

# Globus is not great at determining the url of container a service is running in so that in may
# advertise that. By default it assumes http is used and the port is 8080. These should be
# overridden if this is wrong.

# If specified, it should be http or https. This should be overriden to https if
# are deploying this service into a Globus secured https container.
advertise.container.scheme=http
# Port of web container which hosts this service.
advertise.container.port=8080
# In certain cases even the hostname may be incorrect, this property will override that
advertise.container.hostname=
# Boolean indicating whether to advertise with index services or not
advertise.perform=true

# See previous notes.
host.credential.key=
host.credential.cert=

# Directory to use for storing staging files, this defaults to java.io.tmpdir which is set by
# tomcat to be the directory $CATALINA_HOME/temp
queue.staging.path=${java.io.tmpdir} 
# boolean to determine if staged files should be deleted be deleted after jobs are complete.
queue.staging.clean=true

# Many of the services have a property called *.staging.type
# (e.g. sequest.staging.type, omssa.staging.type), if this is set to
# gridftp staged files are read and written using gridftp. In that
# case gridftp.host and gridftp.prot should be set to control which
# gridftp server these files are sent to.  
gridftp.host=localhost
gridftp.port=2811

systemjobqueue.db.url
systemjobqueue.db.driver
systemjobqueue.db.username
systemjobqueue.db.password
systemjobqueue.db.dialect
systemjobqueue.db.hbm2ddl
systemjobqueue.db.showsql

gramjobqueue.db.url
gramjobqueue.db.driver
gramjobqueue.db.username
gramjobqueue.db.password
gramjobqueue.db.dialect
gramjobqueue.db.hbm2ddl
gramjobqueue.db.showsql

# Addintional GRAM properties are available, but are in flux. Further
# updates will be posted here as we make progress on our GRAM client
# implementation. GRAM is configured in the Spring XML file
# edu/umn/msi/tropix/common/jobqueue/execution/gram/context.xml
# contained in the jar file named tropix-jobqueue.jar, advanced users
# may inspect this file for more information.


scaffold

# This can be system or gridFtp. If this is set to system the files will
# be written directly to the file system. Otherwise they will be read
# and written using gridFtp.
scaffold.staging.type=system
# This can be system or gram. If this is set to system, Java will be used
# to manage the execution queue and will system exec calls to launch
# applications. If this is set to gram, the job queue will be managed by
# GRAM.
scaffold.execution.type=system
# MUST BE SET! Should point to an installed Scaffold executable.
scaffold.path=

sequest

# This can be system or gridFtp. If this is set to system the files will
# be written directly to the file system. Otherwise they will be read
# and written using gridFtp.
sequest.staging.type=system
# This can be system or gram. If this is set to system, Java will be used
# to manage the execution queue and will system exec calls to launch
# applications. If this is set to gram, the job queue will be managed by
# GRAM.
sequest.execution.type=system
# MUST BE SET! Should point to an installed Sequest executable.
sequest.path=
# Number of dta files Sequest is allowed to not process before declaring the
# job a failure.
sequest.allowed.drops=0
# Output format of the sequest logs, these are parsed to determine percent of 
# job complete. The default should work for sequest28 programs. If sequest27 is
# executed via PVM this should be set to PVM_OUTPUT.
sequest.output.type=STANDARD_OUTPUT


xtandem

# This can be system or gridFtp. If this is set to system the files will
# be written directly to the file system. Otherwise they will be read
# and written using gridFtp.
xtandem.staging.type=system
# This can be system or gram. If this is set to system, Java will be used
# to manage the execution queue and will system exec calls to launch
# applications. If this is set to gram, the job queue will be managed by
# GRAM.
xtandem.execution.type=system
# If specified, should point to an installed xtandem executable.
xtandem.path=
# If specified, should point to an X! Tandem XSL stylesheet to apply to 
# apply to X! Tandem results. A default will be installed and should likely
# not be changed because that may make Scaffold unable to parse the results.
xtandem.xsl.path=


rawextract

# This can be system or gridFtp. If this is set to system the files will
# be written directly to the file system. Otherwise they will be read
# and written using gridFtp.
rawextract.staging.type=system

# This can be system or gram. If this is set to system, Java will be used
# to manage the execution queue and will system exec calls to launch
# applications. If this is set to gram, the job queue will be managed by
# GRAM.
rawextract.execution.type=system

# Path to ReAdW executable or script.
rawextract.path=

omssa

# This can be system or gridFtp. If this is set to system the files will
# be written directly to the file system. Otherwise they will be read
# and written using gridFtp.
omssa.staging.type=system
# This can be system or gram. If this is set to system, Java will be used 
# to manage the execution queue and will system exec calls to launch 
# applications. If this is set to gram, the job queue will be managed by
# GRAM.
omssa.execution.type=system

# Tropix wraps a script around omssa in order format FASTA databases
# with the formatdb tools distributed with blast. Out of the box,
# Tropix will attempt to install omssa, blast, and the wrapper
# script. It will however not create any of those if omssa.path is
# specified it will use that executable/script. If omssa.path isn't
# set but blast.home and/or omssa.home are set it will not install
# those programs but instead wrap the script around executables in
# those specified directories.
blast.home
omssa.home
omssa.path

bowtie

# This can be system or gridFtp. If this is set to system the files will
# be written directly to the file system. Otherwise they will be read
# and written using gridFtp.
bowtie.staging.type=system
# This can be system or gram. If this is set to system, Java will be used
# to manage the execution queue and will system exec calls to launch
# applications. If this is set to gram, the job queue will be managed by
# GRAM.
bowtie.execution.type=system
# MUST BE SET! Should point to an installed bowtie executable.
bowtie.path=


itraqquantitation

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