Author: buildbot
Date: Thu May 26 22:41:12 2016
New Revision: 989236
Log:
Staging update by buildbot for taverna
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
websites/staging/taverna/trunk/content/documentation/command-line/index.html
Propchange: websites/staging/taverna/trunk/cgi-bin/
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--- cms:source-revision (original)
+++ cms:source-revision Thu May 26 22:41:12 2016
@@ -1 +1 @@
-1745613
+1745667
Propchange: websites/staging/taverna/trunk/content/
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--- cms:source-revision (original)
+++ cms:source-revision Thu May 26 22:41:12 2016
@@ -1 +1 @@
-1745613
+1745667
Modified:
websites/staging/taverna/trunk/content/documentation/command-line/index.html
==============================================================================
---
websites/staging/taverna/trunk/content/documentation/command-line/index.html
(original)
+++
websites/staging/taverna/trunk/content/documentation/command-line/index.html
Thu May 26 22:41:12 2016
@@ -4,7 +4,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
- <title>Apache Taverna - Command Line Tool</title>
+ <title>Apache Taverna - Command-line Tool</title>
<meta http-equiv="Content-Type" content="text/html;charset=UTF-8">
<meta property="og:image" content="/img/taverna-logo-145x134.png" />
@@ -32,7 +32,7 @@
"@context" : "http://schema.org";,
"@type" : ["CreativeWork"],
"@id": "",
- "name" : "Command Line Tool",
+ "name" : "Command-line Tool",
"publisher" : {
"@type" : "Organization",
"url" : "http://www.apache.org/";,
@@ -170,7 +170,7 @@
<div id="page" class="container">
- <h1>Command Line Tool</h1>
+ <h1>Command-line Tool</h1>
<div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
Taverna is transitioning to the Apache Incubator.
@@ -190,139 +190,164 @@ Instead it shows <a class="alert-link" h
visibility: hidden;
}
h2:hover > .headerlink, h3:hover > .headerlink, h1:hover > .headerlink,
h6:hover > .headerlink, h4:hover > .headerlink, h5:hover > .headerlink,
dt:hover > .elementid-permalink { visibility: visible }</style>
-<p>Command Line Tool is a script that runs Taverna workflows from a terminal.
-It comes in a form of a command line script called <em>executeworkflow</em>
- (<em>executeworkflow.bat</em> on Windows and <em>executeworkflow.sh</em> on
Linux/UNIX).</p>
-<p>You can <a href="/download/commandline/">download the Command Line Tool</a>
from the Taverna Web site
- or use the <em>executeworkflow.sh</em> or <em>executeworkflow.bat</em> that
comes
- bundled with the Taverna Workbench installation.</p>
+<p>The Apache Taverna Command-line Tool is a script that runs Taverna workflows
+from a terminal. The command-line script is called <em>executeworkflow</em>
+ (<em>executeworkflow.bat</em> on Windows and <em>executeworkflow.sh</em> on
Linux/UNIX).</p>
+<p>You can <a href="/download/commandline/">download the Command-line Tool</a>
from the
+Taverna Web site or use the <em>executeworkflow.sh</em> or
<em>executeworkflow.bat</em>
+that is bundled with the Taverna Workbench installation.</p>
<ul>
<li><a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Extended+version";>Extended
version</a></li>
</ul>
-<h2
id="what-is-the-difference-between-the-bundled-and-standalone-executeworkflow"><img
alt="" src="/img/information.png" />What is the difference between the bundled
and standalone executeworkflow?<a class="headerlink"
href="#what-is-the-difference-between-the-bundled-and-standalone-executeworkflow"
title="Permanent link">¶</a></h2>
+<h2
id="what-are-the-differences-between-the-bundled-and-standalone-versions"><img
alt="" src="/img/information.png" />What are the differences between the
bundled and standalone versions?<a class="headerlink"
href="#what-are-the-differences-between-the-bundled-and-standalone-versions"
title="Permanent link">¶</a></h2>
<ul>
<li>
-<p>The standalone command line tool has a <strong>separate
configuration</strong>
- <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory";>home
directory</a>,
- called <em>taverna-cmdline-2.x.x</em> - while the bundled tool uses the
same configuration from
- <em>taverna</em> as the Taverna Workbench.</p>
+<p><strong>Versions use different configuration directories.</strong> The
standalone
+ command-line tool stores its configuration settings in a
<strong>separate</strong>
+<a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory";>home
directory</a>,
+called <em>taverna-cmdline-2.x.x</em> - while the bundled tool uses the same
+directory and settings as the Taverna Workbench.</p>
</li>
<li>
-<p>Any <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/HTTP+proxy+preferences";>proxy
settings</a>
- have to be configured manually - copy
- <em>conf/HttpProxy-B307A902-F292-4D2F-B8E7-00CC983982B6.config</em>
from a configured
- Workbench home directory.</p>
+<p><strong>Manually configure proxy settings.</strong> Any <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/HTTP+proxy+preferences";>proxy
settings</a>
+must be manually configured.
+Copy <em>conf/HttpProxy-B307A902-F292-4D2F-B8E7-00CC983982B6.config</em> from a
+configured Workbench home directory.</p>
</li>
<li>
-<p>The bundled tool will load all the <strong>plugins</strong> installed for
the workbench,
- including third-party plugins.
- However it will also load various GUI-supporting functions which might
consume extra memory.</p>
+<p><strong>Bundled tool may use more memory.</strong> The bundled tool will
load all
+installed workbench plugins, including third-party plugins.
+However, it will also load various GUI-supporting functions,
+which may consume extra memory.</p>
</li>
<li>
-<p>To install service plugins for the command line tool, one will have to
manually edit the
- <em>plugins/plugins.xml</em> of the installation or home directory.
- The <em><plugin>... </plugin></em> block can be copied from the
<em>plugins/plugins.xml</em> from
- the <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory";>home
directory</a>
- of a Workbench installation where the plugin is installed.</p>
+<p><strong>Installing service plugins.</strong> To install service plugins for
the
+command-line tool, manually edit the <em>plugins/plugins.xml</em>
+in the installation or home directory. The <code><plugin>...
</plugin></code> block
+can be copied from the <em>plugins/plugins.xml</em> in the <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+home+directory";>home
directory</a>
+of a Workbench installation where the plugin is installed.</p>
</li>
<li>
-<p>The standalone installation and download is smaller than the workbench -
but keeping both
- installed will use more disk space.
- (Note: the command line tool could use the {repository}} folder from the
workbench using
- symlinks or modifiying <em>plugins/plugins.xml</em></p>
+<p><strong>Disk space considerations.</strong> The standalone installation and
download
+is smaller than the workbench - but keeping both the standalone and embedded
+versions installed will use more disk space than the workbench version alone.
+(Note: the command-line tool could use the {repository}} folder
+from the workbench using symlinks or modifiying
<em>plugins/plugins.xml</em>.)</p>
</li>
<li>
-<p>The standalone tool can easily be installed and used on remote servers
without GUI access.</p>
+<p><strong>Standalone version has remote capability, GUI not
required.</strong> The
+standalone version can easily be installed and used on remote servers without
+GUI access.</p>
</li>
<li>
-<p>Running the embedded tool with the database and provenance enabled allows
the command line
- runs to show up in the workbench
- "<a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective";>Workflow
runs</a>".</p>
+<p><strong>With embedded version, runs can show up in workbench.</strong>
Running the embedded
+version with the database and provenance enabled allows the command-line runs
+to show up in the workbench as
+"<a
href="http://dev.mygrid.org.uk/wiki/display/tav250/Result+Perspective";>Workflow
runs</a>."
+<strong>However,</strong> <em>if database and provenance are enabled</em> and
the workbench is
+already running, the command-line tool must use the <em>-clientserver</em>
option.
+Alternatively, if the workbench is shut down, the command-line tool must use
+either a standalone <em>-startdb</em> database server process or the
<em>-embedded</em> option.</p>
</li>
<li>
-<p>On the other hand the tool will have to use <em>-clientserver</em> if the
workbench is already
- running, or if shut down either a standalone <em>-startdb</em> database
server process or
- <em>-embedded</em>.</p>
-</li>
-<li>
-<p>The standalone tool would not be in conflict with the database of the
workbench
- (as it's in a different home directory) - but could be in conflict with
parallel runs of
- the command line tool - in which case a separate <em>-startdb</em>
process should be started with
- the other calls using <em>-clientserver</em> - see
- <a href="#CommandLineTool-Runningthescriptwithdatabase">#Running the
script with database</a></p>
+<p><strong>Potential conflicts.</strong> Although the standalone version would
not be in
+conflict with the workbench database (as it's in a different home directory),
+it could be in conflict with parallel runs of the command-line tool.
+In this case, a separate <em>-startdb</em> process should be started with the
+other calls using the <em>-clientserver</em> option. See
+<a href="#CommandLineTool-Runningthescriptwithdatabase">#Running the script
with a database</a></p>
</li>
</ul>
<p><a name="CommandLineTool-ExecuteworkflowScript"></a></p>
<h2 id="executeworkflow-script">Executeworkflow Script<a class="headerlink"
href="#executeworkflow-script" title="Permanent link">¶</a></h2>
-<p>To get help and a full set of options for the executeworkflow script type
the following in the
- command prompt:</p>
+<p>To get help and a full set of options for the executeworkflow script,
+type the following at the command prompt:</p>
<blockquote>
<p>$ sh executeworkflow.sh -help</p>
</blockquote>
-<p>It will give the following usage options:</p>
+<p>This command will list the following usage options:</p>
<pre>usage: executeworkflow [options] [workflow]
- -clientserver connects as a client to a
- derby server instance.
+
+ -clientserver Connects as a client to a
+ Derby server instance.
+
-cmdir <Credential Manager's directory path> Absolute path to the
directory on the disk
where Credential Manager's
- files are located
+ files are located.
+
-cmpassword Indicates that the master
password for Credential
Manager will be provided
- on standard input
- -dbproperties <filename> loads a properties file
to
- configure the database
- -embedded connects to an embedded
+ on standard input.
+
+ -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
+ prevent multiple
+ 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
+ improvements, 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
- -janus <file> saves Janus RDF/XML trace
+ expected to receive a list.
+
+ -inputdoc <document> Loads inputs from a
Baclava
+ document.
+
+ -inputfile <inputname filename> Loads the named input
from
+ file or URL.
+
+ -inputvalue <inputname value> Directly uses the value
for
+ the named input.
+
+ -janus <file> Saves Janus RDF/XML trace
of execution to FILE or
- 'provenance-janus.rdf'
- -logfile <filename> the logfile to which more
+ 'provenance-janus.rdf'.
+
+ -logfile <filename> Creates logfile to which
more
verbose logging will be
- written to
- -opm <file> saves Open Provenance
+ written.
+
+ -opm <file> Saves Open Provenance
Model (OPM) RDF/XML trace
of execution to FILE or
- 'provenance-opm.rdf'
- -outputdir <directory> save outputs as files in
- directory, default is to
+ 'provenance-opm.rdf'.
+
+ -outputdir <directory> Save output 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
+ workflowName_output.
+
+ -outputdoc <document> Saves output to a new
+ Baclava document.
+
+ -port <portnumber> Returns port number that
+ 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
+
+ -provenance Generates provenance
information and stores it
in the database.
- -startdb automatically starts an
+
+ -startdb Automatically starts an
internal Derby database
server.
@@ -330,61 +355,82 @@ It comes in a form of a command line scr
</pre>
-<p>If this directory already exists then an new directory is created, and
appended with
- <em>_<n></em>, where <em>n</em> is incremented to the next available
index.</p>
-<p>Results are written out to files named after the output port for that
result.
-If a result is composed of lists, then a directory is created for the output
port and
- individual list items are named after the list element index (with 1 being
the first index).
-The the output is the result of an error, the filename is appended with
â.errorâ.</p>
-<p>You can provide your own output directory with the <em>-outputdir</em>
option.
-There will be an error if the directory already exists.</p>
-<p>You can
- <a
href="http://dev.mygrid.org.uk//wiki/display/tav250/Provenance+export+to+OPM+and+Janus";>export
the provenance</a>
+<h3 id="creating-or-exporting-files-and-directories">Creating or exporting
files and directories<a class="headerlink"
href="#creating-or-exporting-files-and-directories" title="Permanent
link">¶</a></h3>
+<p>If this directory already exists, then a new directory is created and
appended
+with <em>_<n></em>, where <em>n</em> is incremented to the next
available index.</p>
+<p>Results are written to files named after the output port for that result.
+If a result is composed of lists, then a directory is created for the output
+port and individual list items are named after the list element index
+(with 1 being the first index). If the output is the result of an error,
+the filename is appended with â.errorâ.</p>
+<p>You can provide your own output directory with the <em>-outputdir</em>
option.
+(There will be an error if the directory already exists.)</p>
+<p>You can
+ <a
href="http://dev.mygrid.org.uk//wiki/display/tav250/Provenance+export+to+OPM+and+Janus";>export
provenance</a>
using the <em>-opm</em> or <em>-janus</em> options.</p>
-<p>You can also record your results to a Baclava document using
<em>-outputdoc</em> option.
-The document will be overwritten if it already exists.
-You can use the <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/DataViewer+Tool";>DataViewer
Tool</a>
- to view Baclava files.</p>
-<p>Inputs can be provided in three ways.
-Both <em>-inputfile</em> and <em>-inputvalue</em> options can be used
together; <em>-inputdoc</em> option must be
- used on its own.
-<em>-inputfile</em> and <em>-inputvalue</em> options both take two additional
arguments, the name of the port
- for the input, and either a file containing the input data, or the input
value itself
- respectively.</p>
-<p>If one of more of you workflow inputs is described as a list, you can
create a list by using
- the <em>-inputdelimiter</em> option, which may be used with either
<em>-inputfile</em> or
- <em>-inputvalue</em>.
-This option takes two parameters â an input name and the delimiter by which
to split the input
- into a list.</p>
-<p>The delimiter may be a simple character, such as a comma or a new-line
character,
- or a regular expression.
-The input string, or file, will then be converted into a list being split by
the delimiter
- specified. </p>
-<p>If a list of greater depth (i.e. a list or lists or deeper) is required
then you will need to
- use the <em>-inputdocoption</em> to pass data from a Baclava file.
-However, if you provide an input of lower depth to that required, then it will
automatically be
- wrapped in one or more lists up to the required depth.
-Providing an input of greater depth than that required will result in an
error. </p>
-<p><a name"CommandLineTool-Runningthescriptwithdatabase"></a></p>
-<h3 id="running-the-script-with-database">Running the script with database<a
class="headerlink" href="#running-the-script-with-database" title="Permanent
link">¶</a></h3>
-<p>If a workflow has a high memory requirement, then it may be better to run
it using a database
- to store data rather than storing it in memory, which is the default
option.
-There are three options for using a database: </p>
+<p>You can also record your results to a Baclava document using
<em>-outputdoc</em> option.
+The document will be overwritten if it already exists.
+(You can use the <a
href="http://dev.mygrid.org.uk/wiki/display/tav250/DataViewer+Tool";>DataViewer
Tool</a>
+ to view Baclava files.)</p>
+<h3 id="inputting-data">Inputting data<a class="headerlink"
href="#inputting-data" title="Permanent link">¶</a></h3>
+<p>Inputs can be provided in three ways.</p>
<ul>
-<li><em>-embedded</em> option, runs with an embedded database.
- This is slightly faster than -clientserver option (below), but has the
limitation that only
- one <em>executeworkflow</em> script may be executed simultaneously.</li>
-<li><em>-clientserver</em> option allows the workflow to be executed backed by
the database running as
- a server.
- By default a database is not started for you, but may be started using
<em>-startdb</em> option.</li>
-<li><em>-startdb</em> option starts a database. It may be used without
providing a workflow to allow
- a database to be started separately, allowing multiple simultaneous
<em>executeworkflow</em>
- script runs.</li>
+<li>
+<p><strong>-inputdoc.</strong> <em>-inputdoc</em> option must be
+ used on its own.</p>
+</li>
+<li>
+<p><strong>-inputfile.</strong> May be used with <em>-inputvalue.</em>
Requires two additional
+arguments: input port name and input filename.</p>
+</li>
+<li>
+<p><strong>-inputvalue.</strong> May be used with <em>-inputfile.</em>
Requires two additional
+arguments: input port name and input value.</p>
+</li>
+</ul>
+<h3 id="creating-a-list">Creating a list<a class="headerlink"
href="#creating-a-list" title="Permanent link">¶</a></h3>
+<p>If one or more of your workflow inputs is described as a list,
+you can create a list using the <em>-inputdelimiter</em> option. This option
+may be used with either <em>-inputfile</em> or <em>-inputvalue</em>.</p>
+<p>The <em>-inputdelimiter</em> option takes two parameters: an input name
+and the delimiter used to split the input into a list.
+The delimiter may be a simple character, such as a comma or a
+new-line character, or a regular expression. The input string (or file)
+will then be converted into a list using the specified delimiter.</p>
+<p>If a list of greater depth is required (i.e., a list or lists or deeper)
+then you will need to use the <em>-inputdocoption</em> to pass data
+from a Baclava file. However, if you provide an input of lower depth than
+what is required, it will automatically be wrapped in one or more
+list levels up to the required depth.
+Providing an input of greater depth than that required will result in an
error.</p>
+<p><a name="CommandLineTool-Runningthescriptwithdatabase"></a></p>
+<h2 id="running-the-script-with-a-database">Running the script with a
database<a class="headerlink" href="#running-the-script-with-a-database"
title="Permanent link">¶</a></h2>
+<p>Storing data in memory is the default option. If a workflow has a high
memory
+requirement, then it may be better to store data in a database.
+There are three options for using a database:</p>
+<ul>
+<li>
+<p><strong>-embedded</strong> option, runs with an embedded database.
+This is slightly faster than the -clientserver option (below), but only one
+<em>executeworkflow</em> script may be executed at a time. (Simultaneous runs
are not
+allowed.)</p>
+</li>
+<li>
+<p><strong>-clientserver</strong> option, allows the workflow to be executed,
backed by the
+database running as a server. By default a database is not started for you.
+You may start a database using the <em>-startdb</em> option.</p>
+</li>
+<li>
+<p><strong>-startdb</strong> option, starts a database. It may be used without
providing
+ a workflow to allow a database to be started separately. In this manner,
+ you can have multiple simultaneous <em>executeworkflow</em> script runs.</p>
+</li>
</ul>
-<p>More advanced database configurations can be specified using
<em>-dbproperties</em> option,
- allowing you to take full control over the database used.
-This takes a second argument, the filename of the propeties file, for which
the following
- example contains the default settings used: </p>
+<h3 id="advanced-database-operations">Advanced database operations<a
class="headerlink" href="#advanced-database-operations" title="Permanent
link">¶</a></h3>
+<p>Advanced database configurations can be specified using the
+<em>-dbproperties</em> option, allowing you to take full control over the
database used.
+This takes a second argument, the filename of the properties file. Below are
+the default settings for the properties file.</p>
<pre>
in_memory = true
provenance = false
@@ -396,22 +442,25 @@ driver = org.apache.derby.jdbc.EmbeddedD
jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
</pre>
-<p>If you want to run the Derby database with client/server setting instead of
with the embedded
- driver, change the properties in the <em>-dbproperties</em> file (described
above) as follows:</p>
+<h3 id="use-derby">Use Derby<a class="headerlink" href="#use-derby"
title="Permanent link">¶</a></h3>
+<p>If you want to run the Derby database with client/server setting instead
+of with the embedded driver, change the properties in the
<em>-dbproperties</em>
+file (described above) as follows:</p>
<pre>
driver=org.apache.derby.jdbc.ClientDriver
start_derby=true
</pre>
-<p>If you wish to run your own separate Derby server instance, then do not
define the
- <em>start_derby</em> option and define the port on which you are running
you Derby server as
- <em>port=<port></em>. </p>
-<p>If you want to use MySQL database rather than Derby, first you need to drop
the
- mysql-connector-java-5.1.5.jar file from the
- <a href="http://dev.mysql.com/downloads/connector/j/";>mySQL</a> website
into the lib folder of the
- Taverna installation directory (Taverna installation directory if where you
are running the
- script from). </p>
-<p>You need to edit the <em>-dbproperties</em> file as follows: </p>
+<p>If you want to run your own separate Derby server instance, then do not
+define the <em>start_derby</em> option and instead define your Derby server
port
+as <em>port=<port></em>.</p>
+<h3 id="mysql">MySQL<a class="headerlink" href="#mysql" title="Permanent
link">¶</a></h3>
+<p>If you want to use MySQL rather than Derby, first copy the
+mysql-connector-java-5.1.5.jar file from the
+<a href="http://dev.mysql.com/downloads/connector/j/";>mySQL</a> website into
the lib folder
+of the Taverna installation directory. (The Taverna installation directory is
+where you are running the script.)</p>
+<p>Edit the <em>-dbproperties</em> file as follows:</p>
<pre>
connector=mysql
jdbcuri=jdbc:mysql://localhost/T2Provenance
@@ -422,53 +471,63 @@ password=<password>
port=<port>
</pre>
-<p>It is essential that the database name in the <em>jdbcuri</em> property is
T2Provenance,
- as this database is hard-coded into the MySQL provenance SQL queries. </p>
-<p>If you do not specify the port, the script will try to connect to the
default port for MySQL
- server, which is 3306. </p>
+<p>Important: The database name in the <em>jdbcuri</em> property <strong>must
be</strong> T2Provenance,
+as this database name is hard-coded into the MySQL provenance SQL queries.</p>
+<p>If you do not specify the port, the script will try to connect to the
default
+port for MySQL server, which is 3306.</p>
<blockquote>
<p><img alt="" src="/img/warning.png" /> When using <em>-dbproperties</em>
together with other
options, the other options take precedence.</p>
</blockquote>
<p><a name=CommandLineTool-Examples"></a></p>
<h2 id="examples">Examples<a class="headerlink" href="#examples"
title="Permanent link">¶</a></h2>
-<p>Some examples on how the script can be invoked are shown below. </p>
+<p>Workflows names are listed at the end of the command, after any options.
+You must enclose file paths and input values in quotes if they contain spaces.
+Examples are shown below.</p>
+<h3 id="example-1">Example 1<a class="headerlink" href="#example-1"
title="Permanent link">¶</a></h3>
<blockquote>
<p>$ sh executeworkflow.sh "/Users/alex/Taverna
Workflows/wf-1.t2flow"</p>
</blockquote>
-<p>The above line executes the workflow located in <em>/Users/alex/Taverna
Workflows/wf-1.t2flow</em>
- that has no inputs and uses the memory for data storage (the default
option).
-Make sure to enclose the file path in quotes if it contains spaces.
-The <em><workflowName>_outputdirectory</em> will be created in the
current directory and outputs
- will be written to it. </p>
+<p>The command in Example 1 executes the workflow located in
+<em>/Users/alex/Taverna Workflows/wf-1.t2flow</em>.
+It has no input values and uses memory for data storage (the default option).
+Because no output directory is specified, a subdirectory for output files
+(<em><workflowName>_outputdirectory</em>) will be created under the
current
+directory.</p>
+<h3 id="example-2">Example 2<a class="headerlink" href="#example-2"
title="Permanent link">¶</a></h3>
<blockquote>
<p>$ sh executeworkflow.sh -embedded -inputvalue in1 aaa -inputvalue in2
"bb b" -outputdir /tmp/wf-2/ wf-2.t2flow</p>
</blockquote>
-<p>The above line executes the workflow <em>wf-2.t2flow</em> from the current
directory passing the value
- âaaaâ to the input port <em>in1</em> and value âbb bâ to the input
port <em>in2</em>.
-If input values contain spaces make sure to enclose them in quotes.
-Uses the embedded Derby database to store the data.
-Outputs will be written to the <em>/tmp/wf-2/</em> directory. </p>
+<p>The command in Example 2 executes the workflow <em>wf-2.t2flow</em> from
the current
+directory and uses the embedded Derby database to store the data.
+It passes the value âaaaâ to input port <em>in1</em> and the value âbb
bâ
+to input port <em>in2</em>. Output files will be written to the
<em>/tmp/wf-2/</em>
+directory.</p>
+<h3 id="example-3">Example 3<a class="headerlink" href="#example-3"
title="Permanent link">¶</a></h3>
<blockquote>
<p>$ sh executeworkflow.sh -inputvalue in1 aaa -inputfile in2 input2.txt
-inputdelimiter in2 "\n" wf-3.t2flow</p>
</blockquote>
-<p>The above line executes the workflow <em>wf-3.t2flow</em> from the current
directory passing the value
- âaaaâ to the input port <em>in1</em> and splitting the content of file
<em>input2.txt</em> using â\nâ
- (new line character) as the delimiter and passing the resulting list to the
input port <em>in2</em>.
-Make sure to out the delimiter in quotes, even if it is just a single
character, like â;â.
-The <em><workflowName>_outputdirectory</em> will be created in the
current directory and outputs
- will be written to it. </p>
+<p>The command in Example 3 executes the workflow <em>wf-3.t2flow</em> from
the current
+directory, passing the value âaaaâ to input port <em>in1</em>. It splits
the
+contents of file <em>input2.txt</em> using â\nâ (new line character) as
the delimiter
+and passes the resulting list to input port <em>in2</em>.
+<strong>NOTE: The delimiter must be in quotes</strong>, even if it is a single
+character, such as â;â.
+The <em><workflowName>_outputdirectory</em> subdirectory will be created
+under the current directory and will contain all output files.</p>
+<h3 id="example-4">Example 4<a class="headerlink" href="#example-4"
title="Permanent link">¶</a></h3>
<blockquote>
<p>$ sh executeworkflow.sh -inputdoc /tmp/input-doc.xml -outputdoc
/tmp/output-doc.xml "/Users/alex/Taverna
Workflows/wf-4.t2flow"</p>
</blockquote>
-<p>The above line executes the workflow <em>/Users/alex/Taverna
Workflows/wf-4.t2flow</em>, loading
- inputs from the Baclava document in <em>/tmp/input-doc.xml</em>, and
writing the outputs to a
- Baclava document <em>/tmp/output-doc.xml</em>. </p></div>
+<p>The command in Example 4 executes the workflow
+<em>/Users/alex/Taverna Workflows/wf-4.t2flow</em>,
+loading inputs from the Baclava document in <em>/tmp/input-doc.xml</em>, and
creating
+a Baclava document in the output directory:
<em>/tmp/output-doc.xml</em>.</p></div>
</div>
