Daemon
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Phenyx Daemon requirements
Windows platform
Java >= 1.5
Internet connection to a Phenyx server (for job submissions)
How to install Phenyx Daemon
- download from http://downloads.phenyx-ms.com
- unzip the phenyx-daemon.zip file
- launch phenyx.exe
Get and install your Phenyx Daemon license
- You need a valid license to run the daemon. To generate your license, get it from the license Information menu (see image below). Please send us hostID information (named XXXXXX in the image below) at mailto:support@phenyx-ms.com
- you will receive a .lic file to insert into the phenyx-daemon directory
- Exit and launch again phenyx.exe
How to do batch submissions
- Quick overview with the Phenyx Daemon Tutorial Movie http://www.phenyx-ms.com/_library/phenyx_daemon/phenyx_daemon.htm
Access the batch submission page
- From the top menu, go to Actions > Batch Submission
Select a workflow to process
- Select one of the predefined workflow
- The available workflows are listed, select one to see a short process description on the right-hand side.
- Note: in the default list of available workflow, one does requires Phenyx (or at least one portion of it) to be installed locally: filter, zip and submit. It calls the convertspectra.pl script locally before connecting to a Phenyx server.
Select a Phenyx session
- Select a predefined session from the drop down menu.
Select a submission profile
- Once you have selected a Phenyx session, click on the refresh link to have the user's profiles listed.
Root name for the batch
- Free text field to name a batch and help to retrieve a job in the Phenyx Desktop page
Select the mode to process data
- Directory watch, to watch the contain of a directory and to automatically submit a new available datafile (already submitted datafiles are tagged in order not to be twice submitted)
- click on the browse link to select another directory
- clik on the start to watch directory to run automatically the jobs
- Caution: you can remove tagged files, but once done, all the files present in the directory will be submitted
- Drop files, to directly submit a datafile
Accepted formats
Phenyx Daemon currently accepts:
- .dta
- .mgf
- .mzData
Compressed files are accepted as .zip archives, if the file format is specified
- test.mgf.zip will be accepted
- test_mgf.zip will be rejected
Likewise
- test.mgf.txt will be accepted
- test.txt will be rejected
Add new Submission sessions, Submission profiles and workflows
Add new Submission sessions
- If you want to create a new session,
- Go to Session manager by a) select the create new session in the drop down menu or b) go to Manage > Session Manager >Manage Sessions
- Define the new session
- Session: url of the Phenyx server (you have to specify https:// for secure session ; might contain a port name (:8080))
- Username: Username of the Phenyx account
- Password: Password of the Phenyx account
- For example:
- myName@phenyx.vital-it.ch/pwi
- phenyx.vital-it.ch/pwi
- myName
- myPassWord
- yourname@https://phenyxonline.genebio.com/pwi
- https://phenyxonline.genebio.com/pwi
- yourname
- yourpw
- james@my-local-phenyx.edu:8080/pwi
- my-local-phenyx.edu:8080/pwi
- james
- bond007
Add new Submission profiles
- The list of submission profiles available for the daemon is collected from each user's list on the phenyx server. If you need to create a new submission profile, go to the Phenyx Submission page to edit/create a new profile, as usual.
- Here the link to the User Manual http://phenyx.vital-it.ch//docs/pwi/MSMSIonSearch.html#951451
- Once a new profile is created, click on the refresh link in the daemon batch submission window to update the list.
Add new Workflows
- If you want to add a new workflow, go to the Workflow manager
- a) select open workflow manager in the drop down menu
- or
- b) Manage > Submission> Workflow
- Add a XML workflow file.
- Once a new workflow is added, it will appear in the list of available workflows in the batch submission window.
- Some example workflows can be found at http://downloads.phenyx-ms.com/daemon/workflows/
Specific workflows
- Extract Thermo raw files with extract_msn and submit to Phenyx. This workflow uses Thermo extract-msn to extract peaklists in dta format, then merge the dtas with merge.pl, and then submit the merged file to Phenyx. It is designed to run the Phenyx daemon on a windows computer hosting the MS instrument control/data analysis software.
- Make sure that extract_msn.exe is installed on your computer. If you have a recent version of Xcalibur / Bioworks it is by default available in the C:\Xcalibur\system\programs directory.
- Download and extract the merge.zip file available here in the C:\utils\merge_dta directory (create it if you do not have it). You can alternatively get the merge.pl script from [ftp://ftp.genebio.com/phenyx/others/merge/ here.
- Make sure you have perl installed.
- Install the Thermo-extract_msn-merge-submit.xml workflow file in the daemon (right-click on the hyperlink and save link as xml file).
- Note1: if you need/want to change application file paths, modify them in the workflow xml file accordingly.
- Note2: the workflow file uses the -G0 -S0 options in extract_msn. You can edit them if needed.
- (Xcalibur is a registered trademark and BioWorks is a trademark of Thermo Electron Corporation.)
- Extract Thermo raw files with ReAdW and submit to Phenyx. This workflow uses the Institute for Systems Biology ReAdW.exe application to generate a mzXML file, then compress the file in zip format, and then submit it to Phenyx. It is designed to run the Phenyx daemon on a windows computer hosting the MS instrument control/data analysis software.
- Make sure that Thermo Xcalibur is installed on your computer.
- Download and extract ReAdW from sourceforge. Put the ReAdW.exe file in C:\utils\ReAdW\ directory (create it if you do not have it).
- Install the Thermo-raw-readw-submit.xml workflow file in the daemon (right-click on the hyperlink and save link as xml file).
- Note1: if you need/want to change application file paths, modify them in the workflow xml file accordingly.
How to upgrade Phenyx daemon
Access the Update Manager page
- from the top menu, go to Help > Update Manager
- select Search for updates of the currently installed features.
- click on the Finish button.
- follow the installation instructions.
Troubleshooting
In case an error message appears, please do NOT pass the message (doing OK for instance), but report:
Help > About Phenyx Daemon > Configuration Details > View Error Log
and send us the log at mailto:support@phenyx-ms.com
