| =============================== | |
| Taverna command line tool 2.4.0 | |
| =============================== | |
| http://www.taverna.org.uk/ | |
| http://www.mygrid.org.uk/ | |
| Released by myGrid, 2011-07-14 | |
| (c) Copyright 2005-2011 University of Manchester, UK | |
| Licence | |
| ======= | |
| Taverna is licenced under the GNU Lesser General Public Licence. (LGPL) 2.1. | |
| See the file LICENCE.txt or http://www.gnu.org/licenses/lgpl-2.1.html for | |
| details. | |
| If the source code was not included in this download, you can download it from | |
| http://www.taverna.org.uk/download/workbench/2-3/#download-source or | |
| http://www.taverna.org.uk/download/source-code/ | |
| Taverna uses various third-party libraries that are included under compatible | |
| open source licences such as the Apache Licence. | |
| Documentation | |
| ============= | |
| See http://www.taverna.org.uk/documentation/taverna-2-x/ for | |
| documentation and tutorials on using Taverna. | |
| In particular | |
| http://www.taverna.org.uk/documentation/taverna-2-x/command-line-tool/ | |
| and http://www.mygrid.org.uk/dev/wiki/display/taverna23/Command+Line+Tool | |
| will explain how to use the command line tool. | |
| See http://www.mygrid.org.uk/dev/wiki/display/taverna/User+Manual for the | |
| Taverna 2.4 user manual. | |
| See the file "known-issues.txt" for known issues with this release, and the file | |
| "release-notes.txt" for improvements since the previous version of Taverna. | |
| Usage | |
| ===== | |
| In Windows, execute "executeworkflow.bat", while on OSX/Linux/UNIX, | |
| execute "sh executeworkflow.sh". | |
| On Linux/OSX/UNIX you may set the executable bit using | |
| "chmod 755 executeworkflow.sh", allowing you to execute ./executeworkflow.sh | |
| directly. You can make symlinks to this shell script from /usr/local/bin or | |
| equivalent. | |
| Run executeworkflow with parameter -help for detailed help, also see | |
| http://www.taverna.org.uk/documentation/taverna-2-x/command-line-tool/ | |
| usage: executeworkflow [options] [workflow] | |
| -clientserver connects as a client to a derby | |
| server instance. | |
| -dbproperties <filename> loads a properties file to | |
| configure the database | |
| -embedded connects to an embedded Derby | |
| database. This can prevent | |
| mulitple invocations | |
| -help displays comprehensive help | |
| information | |
| -inmemory runs the workflow with data | |
| stored in-memory rather than in a | |
| database. This can give | |
| performance inprovements, at the | |
| cost of overall memory usage | |
| -inputdelimiter <inputname delimiter> causes an inputvalue or inputfile | |
| to be split into a list according | |
| to the delimiter. The associated | |
| workflow input must be expected | |
| to receive a list | |
| -inputdoc <document> load inputs from a Baclava | |
| document | |
| -inputfile <inputname filename> load the named input from file or | |
| URL | |
| -inputvalue <inputname value> directly use the value for the | |
| named input | |
| -logfile <filename> the logfile to which more verbose | |
| logging will be written to | |
| -outputdir <directory> save outputs as files in | |
| directory, default is to make a | |
| new directory workflowName_output | |
| -outputdoc <document> save outputs to a new Baclava | |
| document | |
| -port <portnumber> the port that the database is | |
| running on. If set requested to | |
| start its own internal server, | |
| this is the start port that will | |
| be used. | |
| -provenance generates provenance information | |
| and stores it in the database. | |
| -startdb automatically starts an internal | |
| Derby database server. | |
| For example: | |
| $ taverna-commandline-2.4.0/executeworkflow.sh Retrieve_sequence_in_EMBL_format.t2flow | |
| Outputs will be saved to the directory: | |
| /home/stain/Desktop/Retrieve_sequence_in_EMBL_format_output | |
| $ cat Retrieve_sequence_in_EMBL_format_output/sequence | |
| ID X52524; SV 1; linear; genomic DNA; STD; INV; 4507 BP. | |
| XX | |
| AC X52524; | |
| XX | |
| DT 20-SEP-1990 (Rel. 25, Created) | |
| DT 18-FEB-1991 (Rel. 27, Last updated, Version 6) | |
| .. | |
| aggttagaaa aaataaataa aaataaaatt gagaagaatg taaattaaat atagaattcg 4500 | |
| agctcgg 4507 | |
| // | |
| You can use full URLs to workflows and inputs, for instance: | |
| http://www.myexperiment.org/workflows/1004/download/retrieve_sequence_in_embl_format_873401.t2flow | |
| Examples | |
| ======== | |
| Example Taverna 2.4 workflows can be found in the myExperiment starter pack at | |
| http://www.myexperiment.org/packs/254 | |
| You can share and find other workflows at http://www.myexperiment.org/ | |
| Support | |
| ======= | |
| See http://www.taverna.org.uk/about/contact-us/ for contact details. | |
| You may email support@mygrid.org.uk for any questions on using Taverna | |
| workbench. myGrid's support team should respond to your query within a | |
| week. | |
| Mailing lists | |
| ------------- | |
| We also encourage you to sign up to the public *taverna-users* mailing list, | |
| where you may post about any problem or give us feedback on using Taverna. | |
| myGrid developers are actively monitoring the list. | |
| * http://lists.sourceforge.net/lists/listinfo/taverna-users | |
| * http://taverna-users.markmail.org/search/?q= | |
| If you are a developer, writing plugins for Taverna, dealing with the code | |
| behind Taverna or integrating Taverna with other software, you might find it | |
| interesting to also sign up for the public *taverna-hackers* mailing list, | |
| where you can also track the latest developments of Taverna. | |
| * http://lists.sourceforge.net/lists/listinfo/taverna-hackers | |
| * http://taverna-hackers.markmail.org/search/?q= | |
| Requirements | |
| ============ | |
| Java | |
| ----- | |
| Taverna requires the Java Runtime Environment (JRE) version 6 or later from | |
| Oracle. No other versions of Java are officially tested with Taverna. | |
| Windows users might need to download Java from http://java.com/ | |
| Linux users have different options to install Java depending on their Linux | |
| distribution. Some distributions, such as Ubuntu, might come with alternative | |
| open source implementations of Java, like Gnu GCJ and OpenJDK. We've identified | |
| some issues with these implementations, and recommend using the official Java | |
| implementation from Sun/Oracle. | |
| To download Oracle Java 6 for Ubuntu, start a Terminal, and type the following: | |
| sudo apt-get install sun-java6-jre | |
| and follow the instructions. You might also need to change the default Java | |
| implementation by running: | |
| sudo update-alternatives --config java | |
| To check your version of Java on the command line, try: | |
| $ java -version | |
| java version "1.6.0_22" | |
| Java(TM) SE Runtime Environment (build 1.6.0_22-b04) | |
| Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode) | |
| Read http://www.taverna.org.uk/download/workbench/system-requirements/ | |
| for more requirement details. | |
| Secure web services | |
| ------------------- | |
| If you need to invoke secure services or access secured data from your | |
| workflows (e.g. if you need to provide username and password to gain access to | |
| your service/data or your service's URL starts with HTTPS), then you need to | |
| allow Taverna to communicate securely to such resources using the strongest | |
| possible cryptography. | |
| To do so, you have to install the 'Unlimited Strength Java Cryptography | |
| Extension' policy instead of the default restrictive policy that is | |
| shipped with Java; the default policy will for export reasons only | |
| allows the use of "weak" cryptography (e.g. short passwords and keys). | |
| Java by default only comes with limited-strength cryptography support | |
| because of import control restrictions in some countries, where | |
| unlimited-strength cryptography is classified as a "weapon technology". | |
| Thus, you must determine whether your country's laws allow you to | |
| install such software and you are responsible for doing so. | |
| The policy files on your system are located in: | |
| <java-home>/lib/security/local_policy.jar | |
| <java-home>/lib/security/US_export_policy.jar | |
| where <java-home> is the jre directory of the Java Development Kit (JDK) or the | |
| top-level directory of the JRE (Java Runtime Environment) on your system. | |
| If eligible, you may download the unlimited strength versions of the above | |
| policy files and replace the ones that were installed by default. This will | |
| effectively "turn on" the use of unlimited-strength security in Java on your | |
| system. Not installing these files will most probably cause invoking of secure | |
| services from Taverna to fail. Note that if you switch to another Java version | |
| you will have to install the policy files again in the appropriate directory of | |
| your new Java installation. | |
| For Java 6, you can download the unlimited cryptography policy jar files from: | |
| http://www.oracle.com/technetwork/java/javase/downloads/index.html | |
| Advanced | |
| ======== | |
| Logging | |
| ------- | |
| You will find detailed logs in Taverna's home directory. You can | |
| view this directory from within Taverna by choosing | |
| Advanced->Show Log Folder in the menu. | |
| See: | |
| Windows XP: C:\Documents and settings\JohnDoe\ | |
| Application Data\taverna-cmd-2.4.0\logs | |
| Vista/Windows 7: C:\Users\JohnDoe\AppData\Roaming\taverna-cmd-2.4.0\logs | |
| OS X: /Users/JohnDoe/Library/Application support/taverna-cmd-2.4.0/logs | |
| Linux: /home/johndoe/.taverna-cmd-2.4.0/logs | |
| Note that "Application data" and "AppData" are hidden folders in Windows. | |
| To modify the log levels, edit "conf/log4j.properties" in the Taverna | |
| installation folder. | |
| Memory usage | |
| ------------ | |
| The Taverna command line tool will by default use a maximum of | |
| 300 MB. | |
| If Taverna happens to run out of memory while running a workflow with | |
| large data by using the option -embedded This will reduce execution speed | |
| slightly, but should consume less memory. | |
| If you need to increase the available memory, edit "executeworkflow.sh" or | |
| "executeworkflow.bat" and replace "-Xmx300m" with say "-Xmx600m" to use | |
| 600 MiB. | |