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compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines
http://compomics.github.io/projects/searchgui.html
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Can't run searchGUI on Linux #327

Closed zys7777 closed 2 years ago

zys7777 commented 2 years ago

I install SearchGUI in conda using the command

conda install -c conda-forge -c bioconda searchgui

And I run

java -cp /myfolder/SearchGUI-3.3.9.jar eu.isas.searchgui.cmd.SearchCLI -spectrum_files "/myfolder/F08_Rep1.mgf" -fasta_file "/myfolder/1.fasta" -output_folder "/myfolder" -id_params "/myfolder/peptideshaker1.par" -xtandem 1 -myrimatch 1 -ms_amanda 1 -msgf 1 -omssa 1 -comet 1 -tide 1 -andromeda 1 -novor 1 -directag 1 -threads 16

The SearchGUI just don't start. Is there anything wrong?

hbarsnes commented 2 years ago

Seems like the version on conda is quite old. Any chance you can rather download the latest version directly?

Windows: https://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/4.1.16/SearchGUI-4.1.16-windows.zip Linux/Mac: https://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/4.1.16/SearchGUI-4.1.16-mac_and_linux.tar.gz

All you have to do is download, unzip and run. And the only requirement is that you have Java installed.

zys7777 commented 2 years ago

It reports error, see below

image

log file:

java.io.FileNotFoundException: conf/databases.xml (No such file or directory) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at java.base/java.io.FileWriter.(FileWriter.java:96) at eu.isas.searchgui.processbuilders.AndromedaProcessBuilder.createDatabaseFile(AndromedaProcessBuilder.java:203) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2308) at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:304) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:343) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834)

hbarsnes commented 2 years ago

Could it be the case that you are running this on Mac or Linux? As Andromeda is only supported in Windows. Try turning off Andromeda (-andromeda 0) and see if that helps?

zys7777 commented 2 years ago

Problem solved. Thanks! You help me a lot.