postgresql/insertFKsCreatePostgreSQLAll.sql (for PostgreSQL) or
oracle/insertFKsCreateOracleAll.sql (for Oracle)
to create some tables
If you are using MySQL InnoDB must be now the default engine. The my.ini (Windows)/ my.cnf (Linux) must contain the following entry: default-storage-engine=INNODB
If not MASPECTRAS won't work properly (For AAS MyISAM is sufficient). To correct enter: default-storage-engine=INNODB. Stop the AAS; Restart MySQL; Start the AAS
7.2. Go to $JBOSS_HOME/bin
7.3. Start maspectras with
run-maspectras.bat (for Windows) or
run-maspectras.sh (for Linux or Solaris)
and wait until the JBoss started
7.4 Use from /database/initialize/maspectras/
mysql/sequestInitialValuesMySQL.sql (for MySQL) or
e.g. /usr/local/mysql/bin/mysql -u maspectras -p maspectras < /home/maspectras/maspectras/database/initialize/maspectras/mysql/sequestInitialValuesMySQL.sql
e.g. Enter password: maspectras
postgresql/sequestInitialValuesPostgreSQL.sql (for PostgreSQL) or
oracle/sequestInitialValues.sql (for Oracle)
to insert required data
8. Change the Maspectras settings and insert the path to the newly created DATAROOTDIRECTORY
8.1. Open http://localhost:8080
8.2. Click on JMX-Console
8.3. Click on service=ServerSettings
8.4. Use the method setProperty
p1 = DATAROOTDIRECTORY
p2 = /home/maspectras/maspectrasdata/
Be sure that there is a trailing '/' for Linux or a trailing '\' for Windows otherwise you will have problems with the upload
8.5. Click on invoke
8.6. To check the properties use method „listProperties“
9. Install JClusterService on a UNIX/Linux system (it's not working under windows and not tested under OSX)
9.1. Create a user under which the jclusterservice should execute the commands
and create a JCLUSTERSERVICEROOTDIRECTORY e.g. /home/maspectras/maspectrasjclusterservice where
the user has access right.
If not already done copy and unpack the maspectras.tar.gz again under the home directory
of the new user. This creates a maspectras directory with all the necessary files.
From there copy all files within maspectras/maspectrasjclusterservice to this directory and make sure that
the user can access the folder. e.g.
groupadd maspectras
useradd -d /home/maspectras -g maspectras maspectras
su - maspectras
mkdir -p /home/maspectras/maspectrasjclusterservice
tar -xzf maspectras.tar.gz
cp -r %extracted path%/maspectrasjclusterservice/* /home/maspectras/maspectrasjclusterservice
chown -R maspectras:maspectras /home/maspectras
# (just to be sure that every file is accessible for the service user execute this command as root)
If you have not already switched to maspectras user, become maspectras user (su - maspectras)
9.2. Edit jboss-4.2.2.GA/server/jclusterservice/deploy/JClusterWS.ear/JClusterWSWeb.war/WEB-INF/server-config.wsdd and change to:
<parameter name="attachments.Directory"
value="%installationpath%/jboss-4.2.2.GA/server/JClusterWS/./deploy/JClusterWS.ear/JClusterWS/./deploy/JClusterWS.ear/JClusterWSWeb.war/WEB-INF/attachments"/>
e.g.
/home/maspectras/maspectras/jboss-4.2.2.GA/server/jclusterservice/deploy/JClusterWS.ear/JClusterWSWeb.war/WEB-INF/attachments
If you change the server ports for jclusterservice in bindings.xml, change also the JNDI URL in this file:
<parameter name="jndiURL" value="jnp://localhost:%your_port%"/>
default is:
<parameter name="jndiURL" value="jnp://localhost:21099"/>
9.3. Adapt the path settings to your local installation in jboss-4.2.2.GA/server/jclusterservice/deploy/JClusterWS.ear/JClusterService.jar/usermanagement-utils.properties
sum_users_filepath=JCLUSTERSERVICEROOTDIRECTORY/config/users.xml
e.g.
sum_users_filepath=/home/maspectras/maspectrasjclusterservice/config/users.xml
9.4. Adapt the path settings to your local installation in jboss-4.2.2.GA/server/jclusterservice/deploy/JClusterWS.ear/JClusterService.jar/cluster.properties
9.4.1. The global path settings:
clusterservicedefinition_path=JCLUSTERSERVICEROOTDIRECTORY/config/clusterservice-definition.xml
job_path=JCLUSTERSERVICEROOTDIRECTORY/jobs
jobdefinitions_path=JCLUSTERSERVICEROOTDIRECTORY/job_definitions
e.g.
clusterservicedefinition_path=/home/maspectras/maspectrasjclusterservice/config/clusterservice-definition.xml
job_path=/home/maspectras/maspectrasjclusterservice/jobs
jobdefinitions_path=/home/maspectras/maspectrasjclusterservice/job_definitions
9.4.2. The queueingsystem specific once:
9.4.2.1. Local execution queue
local_execution_job_template_path=JCLUSTERSERVICEROOTDIRECTORY/template/jms-job-definition
e.g.
local_execution_job_template_path=/home/maspectras/maspectrasjclusterservice/template/jms-job-definition
9.4.2.2. Optional if present ... Sun Grid Engine (SGE)
Adapt the paths to the SGE commands
9.4.2.3. Optional if present ... Portable Batch System (PBS/Torque)
Adapt the paths to the PBS/Torque commands
9.5. Install the following applications:
9.5.1. Database repository management initialization:
9.5.2. NCBI-Blast and NCBI-FormatDB
- download from ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz the ncbi toolkit
- install it according to the README from NCBI under JCLUSTERSERVICEROOTDIRECTORY/applications/bin
- copy "blastall" and "formatdb" from "ncbi/build" into JCLUSTERSERVICEROOTDIRECTORY/applications/bin
- copy the whole "data" directory from "ncbi/data" to the location JCLUSTERSERVICEROOTDIRECTORY/applications/data
9.5.3. CLUSTALW2
- download from ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.5/clustalw-2.0.5-src.tar.gz
- install it according to the instructions from EBI under JCLUSTERSERVICEROOTDIRECTORY/applications/bin/
- copy clustalw2 into JCLUSTERSERVICEROOTDIRECTORY/applications/bin
9.6. Adapt the JCLUSTERSERVICEROOTDIRECTORY/config/clusterservice-definition.xml for your local application installation
9.6.1. Change the REPOSITORYMANAGER service definition:
program-path="JCLUSTERSERVICEROOTDIRECTORY/applications/bin/repomanager"
e.g.
program-path="/home/maspectras/maspectrasjclusterservice/applications/bin/repomanager"
and the path parameter:
<parameter position="0" mandatory="true" name="repository" switch="-r">
<parameter-value isdefault="true">JCLUSTERSERVICEROOTDIRECTORY/repository</parameter-value>
</parameter>
e.g.
<parameter position="0" mandatory="true" name="repository" switch="-r">
<parameter-value isdefault="true">/home/maspectras/maspectrasjclusterservice/repository</parameter-value>
</parameter>
9.6.2. Change the NCBI-BLAST/NCBI-FORMATDB service definition:
program-path="JCLUSTERSERVICEROOTDIRECTORY/applications/bin/blastall"
e.g.
program-path="/home/maspectras/maspectrasjclusterservice/applications/bin/blastall"
and
program-path="JCLUSTERSERVICEROOTDIRECTORY/applications/bin/formatdb"
e.g.
program-path="/home/maspectras/maspectrasjclusterservice/applications/bin/formatdb"
9.6.3. Change the CLUSTALW service definition:
program-path="JCLUSTERSERVICEROOTDIRECTORY/applications/bin/clustalw2"
e.g.
program-path="/home/maspectras/maspectrasjclusterservice/applications/bin/clustalw2"
9.6.4. Change the MASSQUANTIFICATION service definition:
program-path="JCLUSTERSERVICEROOTDIRECTORY/applications/bin/msQuantificationCmd"
e.g.
program-path="/home/maspectras/maspectrasjclusterservice/applications/bin/msQuantificationCmd"
9.6.5. The default installation does not require any queueingsystem or cluster and therefore every service
definition is sent to the built-in local java jms queueing system. If you want to run CLUSTALW,
BLAST- and FORMATDB- jobs on a distributed cluster just adapt the configuration parameters described in
3.2 and change in the service definition the parameter queuetype="jms" to queuetype="sge" or
queuetype="pbs".
In such case the JCLUSTERSERVICEROOTDIRECTORY must be shared (rw) under the same path over all
cluster nodes.
9.7. Adapt on the Maspectras side the paths in DATAROOTDIRECTORY/analyses/partitioning/pipeline.xml
<MCLProgramDirectory>/home/maspectras/mcl</MCLProgramDirectory>
<RemoteBlastDatabaseDirectory>JCLUSTERSERVICEROOTDIRECTORY/tmp/BlastDB</RemoteBlastDatabaseDirectory>
<RemoteBlastExecutableDirectory>JCLUSTERSERVICEROOTDIRECTORY/applications/bin</RemoteBlastExecutableDirectory>
<RemoteInputDirectory>JCLUSTERSERVICEROOTDIRECTORY/tmp/Input</RemoteInputDirectory>
<RemoteResultDirectory>JCLUSTERSERVICEROOTDIRECTORY/tmp/Output</RemoteResultDirectory>
e.g.
<MCLProgramDirectory>/home/maspectras/mcl</MCLProgramDirectory>
<RemoteBlastDatabaseDirectory>/home/maspectras/maspectrasjclusterservice/tmp/BlastDB</RemoteBlastDatabaseDirectory>
<RemoteBlastExecutableDirectory>/home/maspectras/maspectrasjclusterservice/applications/bin</RemoteBlastExecutableDirectory>
<RemoteInputDirectory>/home/maspectras/maspectrasjclusterservice/tmp/Input</RemoteInputDirectory>
<RemoteResultDirectory>/home/maspectras/maspectrasjclusterservice/tmp/Output</RemoteResultDirectory>
and the connection parameter ServerURL and ServerURLPlusUser in DATAROOTDIRECTORY/analyses/partitioning/cluster.properties.
Default connection settings presume that the jclusterservice is running on the same host as maspectras on http. If its
runnning on a different machine replace the http://username:password@localhost:21080 by the proper host and port
parameters in DATAROOTDIRECTORY/analyses/partitioning/cluster.properties . If possible secure the connection via SSL
and replace in ServerURL and ServerURLPlusUser the http by https.
9.8. Start the jclusterservice under $JBOSS_HOME/bin with run-jclusterservice.sh
The jclusterservice can run on a different execution host or a cluster system. In
that way the applications queued and executed there are not influencing the performance
of the webinterface.
10. Installation of the markov cluster
10.1. Download the MCL package from http://micans.org/mcl/ and install it. mcl 1.005, 05-118 has been
tested with Maspectras
Maspectras requires the programs clmformat, mcl, and mcxassemble.
10.2. Specify the path to the MCL package in the pipeline.xml file located in the
$DATAROOTDIRECTORY/analyses/partitioning
directory:
e.g.: /home/maspectras/mcl
Make sure that the maspectras user has access to /home/maspectras/mcl and to $DATAROOTDIRECTORY and that the executables have executable rights
11. Installation of Kalign
Not mandatory for the overall function of MASPECTRAS; it is an additional alignment view of grouped proteins; installation can be performed at a later timepoint.
11.1. Download the Kalign package from http://msa.sbc.su.se/cgi-bin/msa.cgi and install it. Kalign version 2.03
has been tested with Maspectras
11.2. Specify the path to the Kalign executable in the maspectrasSettings.properties file located in the
$DATAROOTDIRECTORY/analyses/partitioning
directory:
e.g.: kalignURL=/home/maspectras/kalign/kalign
Make sure that the maspectras user has access to /home/maspectras/kalign/kalign and to $DATAROOTDIRECTORY and that the executable has executable rights
12. Installation of Muscle
Not mandatory for the overall function of MASPECTRAS; it is an additional alignment view of grouped proteins; installation can be performed at a later timepoint.
12.1. Download the Muscle package from http://www.drive5.com/muscle/ and install it. Muscle version 3.6 and 3.7
have been tested with Maspectras
12.2. Specify the path to the Muscle executable in the maspectrasSettings.properties file located in the
$DATAROOTDIRECTORY/analyses/partitioning
directory:
e.g.: muscleURL=/home/maspectras/applications/bin/muscle
Make sure that the maspectras user has access to /home/maspectras/applications/bin/muscle and to $DATAROOTDIRECTORY and that the executable has executable rights
13. Installation of TCoffee and/or Expresso
Not mandatory for the overall function of MASPECTRAS; it is an additional alignment view of grouped proteins; installation can be performed at a later timepoint.
13.1. Download the TCoffee package from http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html. TCoffee version 8.13
has been tested with Maspectras. In order to use a more light-weight installation install TCoffee first with "./install tcoffee".
TCoffee can be used without Expresso. If you want to install Expresso (you will probably require root priviliges) type "./install expresso",
but be aware of the fact, that Expresso is sending your sequences to EBI. If do not want that, you have to install PDB locally;
please visit the Expresso homepage to get more detailed instructions: http://www.tcoffee.org/Projects_home_page/expresso_home_page.html
13.2. Specify the path to the TCoffee executable in the maspectrasSettings.properties file located in the
$DATAROOTDIRECTORY/analyses/partitioning
directory:
e.g.: tCoffeeURL=/home/maspectras/applications/bin/t_coffee
The executable for TCoffee and Expresso will be the same one
Make sure that the maspectras user has access to /home/maspectras/applications/bin/t_coffee and to $DATAROOTDIRECTORY and that the executable has executable rights
13.3. Just for Expresso
Expresso is sending data to the EBI, and EBI requires a valid e-Mail address. To store the e-Mail address you have to start expresso one time manually.
PATHTOTCOFFEEBINARY/t_coffee ANYARBITRARYFASTAFILE -output=clustalw -mode expresso -outfile=ANYOUTFILE
e.g.
/home/maspectras/applications/bin/t_coffee /home/maspectras/maspectras/doc/testdatabase/karl_04090683392.fa -output=clustalw -mode expresso -outfile=./test2.aln
Expresso will prompt you to enter an e-Mail address; after you have entered it and confirmed it with "Y" you can stop the process. Expresso is now ready to use for MASPECTRAS.
14. GO based grouping
MASPECTRAS comes with a ready to use GO-package
14.1. Copy the go folder in the MASPECTRAS package to any desired location (e.g. /home/maspectras/go)
14.2. Specify the path to the GO-paths in the maspectrasSettings.properties file located in the
$DATAROOTDIRECTORY/analyses/partitioning
directory:
e.g.: oboURL=/home/maspectras/go/Homo_Sapiens/gene_ontology_edit_30.09.2009.obo
ontologySourceURL=/home/maspectras/go/Homo_Sapiens/
15. Get access to the AAS
15.1. Open your Web browser and type http://localhost:17080/UsermanagementWeb
15.2. Login using username: admin password: 12345
(change the password afterwards, since this is the ADMINISTRATOR account for the whole AAS)
15.3. Logout
15.4. Login using username: maspectrasadmin password: 12345
(change the password afterwards, since this is the ADMINISTRATOR account only for maspectras)
16. Get access to Maspectras
16.1. Open your Web browser and type http://localhost:8080/maspectras
16. Test Maspectras
17.1. Open a new browser and type https://maspectras.genome.tugraz.at
17.2. Login as guest user (username: guest ; password: guest)
17.3. In the left menu click "Management" -> "File Upload"
17.4. Click on "Query", type "Name" "=" "ICPL_Protmix_1lizu1he_A_c1_ms2_Mascot" and download the Mascot file (for help see user manual 1.2.1 and 1.2.3)
17.5. Click on "Query", type "Name" "=" "ICPL_Protmix_1lizu1he_A_c1_Centroid" and download the mzXML file containing the raw data (check if the file suffix is mzXML and not mzXML.xml, if not change the suffix to mzXML)
17.6. Logout as guest user and continue working at http://localhost:8080/maspectras
17.7. Upload and initialize the database doc/testdatabase/karl_04090683392.fa with the parsing rules of doc/parsingRules/giDatabase_parserules like in the user manual described at chapter 2.1
17.8. Upload the Mascot file (File Type = mascot) and the mzXML file (File Type = Raw-File) like in the user manual described at chapter 2.2
17.9. When you started the upload of the mzXML file the file is translated into a file format more convenient for calculation. Check the status of this translation at Uploadstatus (user manual 2.3). Wait until "TRANSLATING" is replaced by "TRANSLATION FINISHED"
17.10. Create a new Massspecexperiment (for help see user manual 6.1) and assign the mzXML as RawFile
17.11. Start the parsing of the Mascot file (for help see user manual 6.2)
17.12. When the parsing is finished check your results (for help see user manual 7 and 7.1). In the clustered protein view must be 23 clusters ("Protein Sequence" based clustering selected), then the clustering worked well.
18. Installation of Java3D for the client machine
To use the real 3D view Java3D must be installed on the client machine. To download Java3D visit the web-site http://java.sun.com/products/java-media/3D/download.html. It is recommended to increase the memory size for the applet, for more information visit the Maspectras user manual 7.5.1.
19. Test of external DB information fetch
19.1. Open a new browser and type https://maspectras.genome.tugraz.at
19.2. Login as guest user (username: guest ; password: guest)
19.3. In the left menu click "Management" -> "File Upload"
19.4. Click on "Query", type "Name" "=" "M130-E10-G175-C24-P535-1" and download the Mascot file (for help see user manual 1.2.1 and 1.2.3)
18.5. Click on "Query", type "Name" "=" "IPI_HUMAN_APP_v3.41_20080331" and download the database (for help see user manual 1.2.1 and 1.2.3)
19.6. Logout as guest user and continue working at http://localhost:8080/maspectras
19.7. Upload and initialize the downloaded database IPI_HUMAN_APP_v3.41_20080331 with following settings:
Accession-rule: IPI:(\w+\W?\w*)
Description-rule: [^\ ]* [^\ ]* Gene_Symbol.(.*)
Organism-rule: (leave this input field empty)
URL to database: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=ipi&format=default&style=raw&id=
Parser for URL: IPIParser
19.8. Upload the Mascot file (File Type = mascot) like in the user manual described at chapter 2.2
19.9. Create a new Massspecexperiment
19.10. Start the parsing of the Mascot file (for help see user manual 6.2)
19.11. When the parsing is finished check your results and if external information has been fetched (for help see user manual 7.4).