| By default, the workflow is executed using the -inmemory option, and the |
| results are written out to a directory named after the workflow name. |
| |
| If this directory already exists then a new directory is created, and |
| appended with _<n>, where n is incremented to the next available index. |
| |
| 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 '.error'. |
| |
| You can provide your own output directory with the -outputdir option. There |
| will be an error if the directory already exists. |
| |
| You can also record your results to a Baclava document using -outputdoc |
| option. The document will be overwritten if it already exists. |
| |
| Inputs can be provided in three ways. Both -inputfile and -inputvalue options |
| can be used together; -inputdoc option must be used on its own. -inputfile and |
| -inputvalue 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. |
| |
| If one of more of your workflow inputs is a list, you can create a list |
| input by using the -inputdelimiter option, which may be used with either |
| -inputfile or -inputvalue. This option takes two parameters - an input name |
| and the delimiter by which 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 being split by the delimiter specified. Make sure to |
| put the delimiter character in quotes as it may be interpreted by the shell |
| as a special character, e.g. ;. |
| |
| If a list of greater depth (i.e. a list or lists or deeper) is required then |
| you will need to use the -inputdoc option. 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. |
| |
| 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: |
| |
| -embedded option, runs with an embedded database. This is slightly faster than |
| the -clientserver option (below), but has the limitation that only one |
| executeworkflow script may be executed simultaneously. |
| |
| -clientserver 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 -startdb option. |
| |
| -startdb option starts a database. It may be used without providing a workflow |
| to allow a database to be started separately, allowing multiple simultaneous |
| executeworkflow script runs. |
| |
| More advanced database configurations can be specified using -dbproperties |
| option, allowing you to take full control over the database used. This takes a |
| second argument, the filename of the properties file, for which the following |
| example contains the default settings: |
| |
| in_memory = true |
| provenance = false |
| connector = derby |
| port = 1527 |
| dialect = org.hibernate.dialect.DerbyDialect |
| start_derby = false |
| driver = org.apache.derby.jdbc.EmbeddedDriver |
| jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true |
| |
| Note that when using -dbproperties together with other options, the other |
| options take precedence. |
| |
| -cmdir option lets you specify an absolute path to a directory where |
| Credential Manager's files (keystore and truststore - containing user's |
| credentials and trusted certificates for accessing secure services) are stored. |
| If not specified and the workflow requires access to these files, Taverna will |
| try to find them in the default location in <TAVERNA_HOME>/security somewhere |
| inside user's home directory (depending on the platform). |
| |
| -cmpassword option can be used to tell Taverna to expect the password for the |
| Credential Manager on standard input. If the password is not piped in, Taverna |
| will prompt you for it in the terminal and block until it is entered. Do not |
| enter your password in the command line! If -cmpassword option is not specified |
| and -cmdir option is used, Taverna will try to find the password in a special |
| file password.txt in the directory specified with -cmdir option. |