Sources for plugin tasks
Waters Marketplace - marketplace.waters.com
Requires that you register and log in. Tasks can be 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 current batch file distributed with the data transfer task does not work with remote system that require Windows user names and passwords.
An alternative batch file can be found here: http://pgb.liv.ac.uk/files/symphony/CopyData.zip
Unzip the file to get to the batch file.
The current batch file used by the data transfer task required two arguments: the (source) path of the Waters raw data file and the (destination) path to copy the data to. This alternative batch file extends that with two additional, and optional arguments. These are for the user name and password for connecting to the remote system. If these two additional arguments are not supplied, then the behaviour 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, then the first of these additional arguments will be assumed to be the user name, the second will be assumed to be the password.
Outside of Symphony, the batch file could be called 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, user name is 'lord_commander', password is 'ygritte')
Here is what a task using authentication could look like in Symphony. Note here how the user name and password are 'hard-coded' - i.e. they are set in the task directly, data keys are not used.
In the above example 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 user name and password in the task is that you would not need to enter it for each new pipeline that used the task. The disadvantage is that you would need separate tasks every time you had a different set of authentication credentials to provide, as each task could only provide a pre-set 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 this alternative batch file are designed for the Waters raw data format, i.e. a folder. They will have undefined/unexpected behaviour for items that are not folders. This may crop up in the future when users move more than just raw data around. 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. Of course the user can create whatever they want, though presets for authentication and files/folders could 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 e.t.c.
Here I describe how Symphony can support conversion of Waters data to open formats using MSConvert.
Install ProteoWizard. It can be obtained from here: 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 use 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.
Use : Create Tasks
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 may see how a new task could be created from these to convert to another format that MSConvert supports, or to customise some other thing in the conversion process - see the MSConvert GUI for a full set of possible 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 get the task XML files, in case you do not want to create them yourselves or other reasons:
Use : Create Pipeline
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 - I have not checked this. If so, then the #mzmloutputpath (and similar for MGF and mzXML) may be unnecessary.
Here is the link to get 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