=============================== | |
Taverna command line tool 2.5.0 | |
=============================== | |
http://www.taverna.org.uk/ | |
http://www.mygrid.org.uk/ | |
Released by myGrid | |
(c) Copyright 2005-2014 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/2-5/#download-source or | |
http://www.taverna.org.uk/download/source-code/ | |
If you installed a OS-specific distribution of Taverna it may come | |
bundled with a distribution of OpenJDK. OpenJDK is distributed under the | |
GNU Public License (GPL) 2.0 w/Classpath exception. See jre/LICENSE.txt or | |
http://hg.openjdk.java.net/jdk7u/jdk7u/raw-file/da55264ff2fb/LICENSE | |
for details. | |
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 2.5 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-2.5.0/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 2.5 workflows can be found in the myExperiment starter pack at | |
TODO: Update 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 7. | |
Platform-specific builds of the command-line tool should include a build of | |
OpenJDK, if you are running the platform-independent distribution, you | |
may need to download and install Java, see http://java.com/ | |
Read http://www.taverna.org.uk/download/workbench/system-requirements/ | |
for more requirement details. | |
Secure web services | |
------------------- | |
If you do not use the bundled OpenJDK (which has security enabled by default), | |
you may need to modify your Java installation to enable security. | |
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. | |