This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
how_to:spectrummatchfeeder [2011/03/08 15:12] 132.168.74.230 |
how_to:spectrummatchfeeder [2013/04/11 10:41] 132.168.72.131 |
||
---|---|---|---|
Line 1: | Line 1: | ||
====== How-to populate MSI database with spectrum details ====== | ====== How-to populate MSI database with spectrum details ====== | ||
- | Before exporting a given UserContext to PRIDE XML file, you need to poupulate MSI database with missing spectra. | + | Before [[how_to:exportpride|exporting a given UserContext to PRIDE XML file]], check if the MSI database need to be populated with spectrum details. |
+ | |||
+ | :!: **Since hEIDI 1.11.1, this functionality is no more available from the hEIDI GUI, but has to be executed (outside from hEIDI, see bellow) [by your system administrator]. ** | ||
+ | |||
+ | ===== Import spectrum using tool outside hEIDI [by your system administrator] ===== | ||
+ | |||
+ | To import spectrum detail for a specified context using ''Paloma'' tool, you need to have the context id. This property is accessible in Context property sheet. View in [[how_to:accessproperties|]] page. | ||
+ | |||
+ | * Download Paloma-<version>.zip and unzip to <Paloma-install> directory. (Download is available at the following FTP site : [[ftp://ftp.cea.fr/pub/edyp/heidi]]) | ||
+ | * In command prompt (Run -> Cmd), go to <Paloma-install>/ and run : <code>java -Djava.library.path=./lib -Xms512m -Xmx1024m -classpath ./paloma-<version>.jar cea.edyp.palomae1.MainSpectrumFeeder [OPTIONS]</code> | ||
+ | * -Xmx option allow you to specify amount of memory to use for yhios process. Depending on your system (amount of memory and 32bits or 64bits), you can set more memory : -Xmx4000m for example | ||
+ | * OPTIONS are described if no parameter is specified in command line... Nevertheless, here they are : ''-u <user> -p <password> -url <dbURL> -m <root> [-d <driver>] -cid <context_id>'' where | ||
+ | * <user> : user for DB connection | ||
+ | * <password> : password for DB connection | ||
+ | * <dbURL> : url to DB such as jdbc:postgresql:/ / <server_name>/<DB_Name> | ||
+ | * <root> : Path to mascot data files | ||
+ | * <driver> : Optional, default is Postgresql driver (org.postgresql.Driver) | ||
+ | * <context_id> : Context ID to get spectra for | ||
+ | * You can verify there were no error by opening paloma-<user>.log from <Paloma-install> directory. This file contains lots of information, for debug purpose. | ||
+ | * Search for any "ERROR " string to verify no error occurs. | ||
+ | * You can also see how many mascot dat file were parsed. | ||
+ | |||
+ | Look for entry such has | ||
+ | INFO SpectrumEntriesSearch - The selected context contains 2,686 species and 2,686 spectrum are needed | ||
+ | INFO SpectrumEntriesSearch - Paloma - SpectrumEntriesSearch - identify 44 dat files | ||
+ | INFO SpectrumEntriesSearch - .... featuring 2686 peptides | ||
+ | INFO SpectrumMatchFeeder - Paloma - SpectrumMatchFeeder - will parse 44 dat files | ||
+ | |||
+ | * You will also see "44" entry like ''Parser dat file : XXXXX''. Each followed by ''Parser dat file DONE'' | ||
+ | |||
+ | |||
+ | ===== Import spectrum using hEIDI ===== | ||
+ | |||
+ | :!: **Since hEIDI 1.11.1, this functionality is no more available. Should be reintegrated ... ** | ||
* **After having [[how_to:createproject|created ]]or [[how_to:loadproject|opened an hEIDI project]], [[how_to:opensession|open your MSI session]]** but :!: **Don't forget to __activate__ your hEIDI project**.{{ :how_to:spectrummatchfeeder_menu.png|}} | * **After having [[how_to:createproject|created ]]or [[how_to:loadproject|opened an hEIDI project]], [[how_to:opensession|open your MSI session]]** but :!: **Don't forget to __activate__ your hEIDI project**.{{ :how_to:spectrummatchfeeder_menu.png|}} | ||
+ | * **Check, in Windows Explorer, you have mapped a drive to the Mascot data folder** (\\cp-mascot\data) and you are connected to that folder. | ||
* **Select a UserContext**. It has to be [[how_to:proteingrouping|grouped ]]and [[how_to:savetomsidb|saved to MSIdb]]. | * **Select a UserContext**. It has to be [[how_to:proteingrouping|grouped ]]and [[how_to:savetomsidb|saved to MSIdb]]. | ||
* Select the menu **''MS Identifications->Database Update->Populate with spectra''** | * Select the menu **''MS Identifications->Database Update->Populate with spectra''** | ||
* A dialog will appear on the screen to indicate if spectrum details are missing for this UserContext | * A dialog will appear on the screen to indicate if spectrum details are missing for this UserContext | ||
+ | * **Check the Mascot data root path**. You can use ''\\cp-mascot\data'' or the corresponding Drive Letter you have set up in Windows Explorer, for example ''Y:''. | ||
{{:how_to:spectrummatchfeeder_dialog.png|}} | {{:how_to:spectrummatchfeeder_dialog.png|}} | ||
* If spectrum details are missing, click on ''Ok, populate MSIdb with missing spectra'', else click on ''Do nothing & Close this window'' | * If spectrum details are missing, click on ''Ok, populate MSIdb with missing spectra'', else click on ''Do nothing & Close this window'' | ||
* In case you have clicked ''Yes'', a message will appear when process is finished | * In case you have clicked ''Yes'', a message will appear when process is finished | ||
{{:how_to:spectrummatchfeeder_success.png|}} | {{:how_to:spectrummatchfeeder_success.png|}} | ||
- | |||
- | |||
- | |||
- | |||
- |