MRS Administration
Author: Maarten L. Hekkelman

### Directories

MRS files
Raw files
Parsers
Docroot
Blast cache

### Tools

Clustal Omega
rsync

### Restart

After changing the configuration options you have to restart the server to make sure these changes are taken into effect.

### Server configuration

Address
Port

The base URL is the URL by which users can access this server from outside your domain.

Base URL

By default the client address is recorded in the log file, but if the server is behind a reverse proxy, the last X-Forwarded-For entry might be more informative.

Log Forwarded

### Web Service Locations

Leave empty to disable web service

Search
Blast

Parsers
${parser.id}

### Parser configuration

XML parsers are not configurable in the admin pages yet

Perl based parsers should be edited directly, you can find the file for the `${parser.id}` parser at `${global.dirs['parser'] + '/' + parser.script + '.pm'}`

Formats
${format.id}

### Format specification

ID

### Document layout

Formatting a document can be done using JavaScript plugins. To specify a script for the ${format.id} format choose one from the list here which is based on the files found in `${global.dirs['docroot']}/formats`.

JavaScript

### Links

Create 'live' links in documents based on a regular expression. You can reference captures in the regular expression using the variable names $1 for the first capture, $2 for the second, etc.

Regular Expression | Target Databank | Target ID | Index | Anchor |
--- | --- | --- | --- | --- | ---
|  |  |  |  | Delete
|  |  |  |  | Delete

Databanks
${db.id}${db.id}

### Databank information

ID
Enabled
Name
Info URL

Aliases are used in the Blast form and in creating links between databanks based on the values found in e.g. db_xref records. The name is used in the blast databank popup menu.

Aliases

ID | Name |
--- | --- | ---
|  | Delete
|  | Delete

Add alias

### Data retrieval

Update

The source files are expected to be located relative to the raw directory, unless you enter an absolute path.

Source files

Upstream URL can either be ftp:// or rsync://

Upstream URL
Delete stale files
Recusive (rsync)
Port number (rsync)

### Data processing

Parser

FastA file is needed to be able to use the blast search function.

Create FastA

Filters are optional programs through which the raw data is fed, for the Gene databank you could e.g. enter `/usr/bin/gene2xml -bT` to convert ASN.1 into XML on the fly.

Filter

Formatting can be done with one of the defined formatters, or for XML databanks, with an XML Stylesheet.

Formatter

### Scheduler

Enter the time for daily updates and the week day for weekly updates. Monthly updates are done on the first week day of the calender month.

Enabled
Daily update at
Weekly update on

### Blast Queue

Known jobs
ID | Length | Databank | Status |
--- | --- | --- | --- | ---
There are no known blast jobs.