how_to:spectrummatchfeeder
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how_to:spectrummatchfeeder [2013/01/17 16:38] 132.168.72.131 |
how_to:spectrummatchfeeder [2013/04/11 10:41] (current) 132.168.72.131 |
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| :!: **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]. ** | :!: **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 ===== | + | ===== Import spectrum using tool outside hEIDI [by your system administrator] ===== |
| - | * Download Paloma-<version>.zip and unzip to <Paloma-install> directory. | + | 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. |
| - | * Go to <Paloma-install>/ and run : ''java -Djava.library.path=./lib -Xms512m -Xmx1024m -classpath .\paloma-<version>.jar cea.edyp.palomae1.MainSpectrumFeeder <option>'' | + | |
| - | * In -Xmx option you can specify more memory depending on your system (amount of memory and 32bits or 64bits) : -Xmx4000m ... | + | * 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]]) |
| - | * Option 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 | + | * 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 | * <user> : user for DB connection | ||
| * <password> : password for DB connection | * <password> : password for DB connection | ||
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| * <driver> : Optional, default is Postgresql driver (org.postgresql.Driver) | * <driver> : Optional, default is Postgresql driver (org.postgresql.Driver) | ||
| * <context_id> : Context ID to get spectra for | * <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 ===== | ===== Import spectrum using hEIDI ===== | ||
how_to/spectrummatchfeeder.1358437104.txt.gz · Last modified: 2013/01/17 16:38 by 132.168.72.131
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