Mascot Result Download

This command line tool allows users to download any Mascot result file from any Mascot Server V2.3 or higher. It can be used on any Mascot server, but defaults to the APCF. It is aimed to be used inside the Post-Build step of Mascot Daemon, although nothing stops you using it anywhere else. It is a Windows .NET program. The src is provided to you too.

Please note that Mascot Daemon runs as a process under a different username to you, so that you may not be able to access certain remote drives from within Daemon. You will also need to specify a username/password if the Mascot server has security enabled. If you don't like having your password left in script files, it is possible to 'register' your username/password. If you do this, your password is encrypted and stored in the Registry. You will not need to specify it again if you do this. The best approach to start using this tool is to:

• Download the executable
• Run it from the command line. This will check if there are any problems with Firewalls or Virus Scanners blocking the program. If there is, you may need to make an exception for it.
• If you try to download a file that does not exist or you do not have access to, you will get a "Remote Server Error" message
• Once you are happy it works, you can add it to the Mascot Daemon post-build step.

Using mascotDownloader inside Mascot Daemon, press the "External processes" button.

Find the "After each search" command.

Enter the mascotDownloader command.

Remember to put quote (") characters around any path that has a space in it. i.e. "C:my temp".

• Example: to download result from the WEHI sysbio-msacot server for username "bob" and password "thebuilder", type the following into the window:
• "C:my progmascotDownloader.exe" -uri https://sysbio-mascot.wehi.edu.au/mascot -u bob -p thebuilder -d "C:temp" -f <resultfilepath>
• The order of parameters does not matter.

The full command line options are:

mascotDownload [register] | [-uri <baseURI> ] [-u <username>] [-p <password>] -f <fileList> [-d <downloadDir>]

Where: <baseURI> is the URI of the mascot server. Default value is http://www.apcf.edu.au/mascot

<username> is the Mascot Username if security is enabled.

<password> is the Mascot Password if security is enabled.

<flist> is a comma separated list of full file paths, i.e. E:data2011F0.dat,E:data2011F01.dat

<downloadDir> is the download dir. If not listed, the default dir is the CurrentDirectory

register encrypts the password and saves it in the registry. You do not need to specify a password once you do this. No download occurs if you specify register on the command line.

Examples

Here is an example of running it from Mascot Daemon. Enter a line like this in the external processes box of Daemon:

mascotDownload.exe -f <resultfilepath> -d C:temp -u myMascotUserName -p myMascotPassword

It downloads the result file of the finished Mascot job from APCF server, into c:temp.

Mascot Daemon automatically replaces the string "<resultfilepath>" with the name of the finished result file. 

But to use a different server, specify it with -uri (in this example no username is needed as security is not enabled on this server):

mascotDownload.exe -f <resultfilepath> -d c:simon -uri http://mascot-nosecurity/mascot

If you do not want to have your password in scripts, you can register it:

mascotDownload register -u user -p password

The above encrypts the password and puts it in the PC registry. The user need not specify a password after this. 

mascotDownload -f ..data/20111004/F002797.dat -d c:working -uri http://mascot/mascot

The above uses a server with no security enabled. 

mascotDownload -u username -f ..data/20111004/F002797.dat -d c:working

The above uses the APCF server with a pre-registered username/password.

Downloads

Download mascotDownload.exe

Download the src (MS Visual Studio 2008 project)

Tools

• APLToMGFConverter
• Command line tools