Application attributes describe the application itself and should only be given in an application: definition. The available application attributes are described in detail below.
Attribute definition | Description | Default value |
|---|---|---|
| Short description of the application function |
|
| Standard application group(s) for wossname and GUIs |
|
| Standard application group(s) for wossname and GUIs |
|
| Suitability for launching in a GUI |
|
| Suitability for running in batch |
|
| EMBASSY package name |
|
| Third party tool(s) required by this program |
|
| Estimated maximum CPU usage |
|
| Supplier name |
|
| Version number |
|
| Non-emboss application name for SoapLab |
|
| Non-emboss executable for SoapLab |
|
| Commandline template for SoapLab's ACD files |
|
| Comment for SoapLab's ACD files |
|
Their general format is:
ApplicationAttributeName: "ApplicationAttributeValue"
This is a succinct description of application function and will be printed to screen when the program is run, and when the program is run with the -help qualifier. The documentation: string is also searched by the wossname utility, which finds applications by searching for keywords in the documentation: text and application group. If the documentation: attribute is missing, a warning will be issued when you run the program.
The documentation: string must conform to these conventions:
The text should start with an upper-case letter.
The length should be kept to 63 characters or shorter in order to allow the wossname utility to display each program name and its documentation on one 80-character line.
The text should not end with a '.' character
Any acronyms or abbreviations in the text should be written in upper case. (e.g. "SNPs", "EST", "DNA", "ABI", "SRS", "ASCII", "CDS", "mRNA", "B-DNA", "RNA", "CpG", "ORFs", "MAR/SAR", "PCR", "STS", "REBASE", "SCOP", "PROSITE", "PRINTS", "EMBL", "TRANSFAC", "AAINDEX", "BLAST", "GCG", "EMBOSS")
This allows the EMBOSS programs to be placed into groups or subgroups based on their functionality. Programs in the same sub-group generally do similar things whereas programs in the same group but different sub-group do different things but in the same general area. The groups: string is searched by the wossname program, which, given a keyword, will return all the applications containing that keyword in the groups: text or the documentation: text. The groups: string is also used by the seealso application which takes the name of an EMBOSS program and returns a list of the programs which share some functionality with it.
The groups: attribute is followed by a string value, containing the name of one or more groups and one or more subgroups to which the application belongs. The subgroup(s) are optional, but if specified the group(s) and subgroup(s) must be separated by a colon (:). When an application belongs to more than one group (or subgroup), the group names must be separated by either a comma (,) or semicolon (;).
The general format for the groups: attribute is as follows:
application:ApplicationName[ groups: "GroupName1,GroupName2,...:SubgroupName1,SubgroupName2,..." ]
The groups: string must conform to these conventions:
The group name should, ideally, be taken from a list of standard group names defined in the EMBOSS system file groups.standard in the application ACD file directory (see Section 4.2.4.1, “Application Group Names File (groups.standard)”). New groups can be defined, but the definitions should be sent to the EMBOSS developers so they can be added to the standard set.
Group names can have spaces in them.
Subgroup(s) are optional, but if specified the group(s) and subgroup(s) must be separated by a colon (:).
EMBOSS supports arbitrary numbers of levels of subgroup however several third party interfaces rely upon there being a maximum of 2 levels in total, so do not use more than one :.
When an application belongs to more than one group (or subgroup), the group names must be separated by either a comma (,) or semicolon (;).
A set of keywords describing the application functionality. These are used by the application wossname and by some GUIs to EMBOSS.
This attribute has a value of "Yes" or "No" and reflects the suitability for launching the application in a GUI.
This attribute has a value of "Yes" or "No" and reflects the suitability for launching the application in a batch queue.
Third party tool(s) required by this program. This is used by applications which wrap (call) third party applications and therefore rely on this software being present on the system that is running EMBOSS.
Supplier name, in cases where the application was provided by a body other than the EMBOSS core developers.
Version number of the application in case a different version number than the EMBOSS or EMBASSY package version number is required.
This boolean attribute specifies whether an application is part of EMBOSS or EMBASSY. It is only used by SoapLab
Name of an application that is not part of EMBOSS or EMBASSY. This is used in environments (for example, SoapLab) where applications are defined using the ACD syntax but are not part of EMBOSS or EMBASSY itself.