Sources for plugin tasks
Waters Marketplace - marketplace.waters.com
Register and log in. Tasks are found in the Symphony area.
MS Utils - ms-utils.org - Software List
ProteoWizard - ProteoWizard: Tools
BioConductor - Bioconductor - BiocViews
BioConductor Mass Spec section - Bioconductor - BiocViews
DataTransfer — Alternative Batch File with Windows Authentication
The batch file currently distributed with the data transfer task does not work with remote systems that require Windows usernames and passwords.
Find an alternative batch file here: http://pgb.liv.ac.uk/files/symphony/CopyData.zip
Unzip the file to get to the batch file.
The batch file currently used by the data transfer task requires two arguments: the (source) path of the Waters raw data file and the (destination) path to copy the data to. This alternative batch file adds two additional, and optional, arguments. These are for the username and password for connecting to the remote system. If these two additional arguments are not supplied, the behavior is identical to that of the current batch file (i.e., success with systems that do not require authentication, failure with those that do). If these two arguments are supplied, the first of these additional arguments is assumed to be the username, and the second is assumed to be the password.
Outside of Symphony, the batch file could be named like these examples:
1). CopyData.bat c:\source_location\MSe.raw\ c:\destination_location\MSe.raw\
(no authentication required)
2). CopyData.bat c:\source_location\MSe.raw\ c:\destination_location\MSe.raw\ lord_commander ygritte
(authentication required; username is lord_commander, password is ygritte)
Here is what a task using authentication could look like in Symphony. Note how the username and password are hard-coded—i.e., they are set directly in the task, and data keys are not used.
In the example above, the username and password data keys would need to be set in the pipeline definition itself, or somehow extracted dynamically. The advantage of hard-coding the username and password in the task is that you need not enter it for each new pipeline that uses the task. The disadvantage is that you need separate tasks every time you have a different set of authentication credentials to provide, because each task can provide ony a preset credential.
Here is a link to the task XML for the task that uses data keys: http://pgb.liv.ac.uk/files/symphony/DataTransferAuthentication-datakeys.xml
Here is a link to the task XML for the task that uses hard-coded values: http://pgb.liv.ac.uk/files/symphony/DataTransferAuthentication-hardcoded.xml
IMPORTANT: Both the current batch file and the alternative batch file are designed for the Waters raw data format (i.e., a folder). They will show undefined/unexpected behavior for items that are not folders. This may crop up in the future when users move more than just raw data. Perhaps we need other batch files that work with files (and folders), or perhaps there should be a single batch file that is well designed. The user can of course create whatever they want, though presets for authentication and files/folders would be nice.
ProteoWizard — MSConvert Support
MSConvert is a part of the ProteoWizard project—it allows the conversion of vendor format files (including Waters) to open formats such as mzML, mzXML, MGF, and others.
Here we describe how Symphony can support conversion of Waters data to open formats using MSConvert.
Install ProteoWizard. It can be obtained at http://proteowizard.sourceforge.net/downloads.shtml. It is available for Windows (32-bit/64-bit), Linux (64-bit), and Mac (32-bit), though for Symphony the 32-bit version should be installed. It comes complete with all the appropriate Waters software libraries for reading raw files, so there is no requirement for the Waters software libraries to be installed separately, though many PCs may already have that too.
Make a note of the ProteoWizard installation directory. Usually this is "C:\Program Files (x86)\ProteoWizard\" followed by a version-specific suffix.
Create the tasks in Symphony, making sure that the path to MSConvert.exe is correct/appropriate.
This is the task for converting to MGF:
This is the task for converting to mzML:
This is the task for converting to mzXML:
The task definitions are quite similar. You can see how a new task can be created from these to convert to another format supported by MSConvert, or to customize some other thing in the conversion process. See the MSConvert GUI for a full set of options.
The "#copydatapath" argument here would be the same one that a data transfer task uses. See the pipeline below.
Here are the links to the task XML files, in case you do not want to create them yourself (or other reasons):
This is an example pipeline using the data transfer task and the ConvertToMZML task:
Here is what happens in these two tasks:
-The data transfer task copies data from the #rawdatapath to the #copydatapath.
-The conversion task converts data from #copydatapath to #mzmloutputpath.
It may be possible to omit the '-o' option from MSConvert (we have not checked this). If so, then the #mzmloutputpath (and similarly for MGF and mzXML) may be unnecessary.
Here is the link to the pipeline XML file, in case you do not want to create it yourself (or other reasons): http://pgb.liv.ac.uk/files/symphony/DataTransferTraining.xml
Active Preheater, isopropanol