My name is Charlie Sun and I am a bioinformatics software developer working
in NIH-NIAID in united states. I am currently working on a web application
project for Papillomavirus genomic resource data. Here is the link to our
website:
Pave.niaid.nih.gov <http://pave.niaid.nih.gov/>
I am adding some analysis tools including MSA to Pave and we decided to use
Jalview to visualize the results. One feature requested is generating eps
file for download. I installed the Jalview desktop version and tried to run
it in the command line mode to generate eps file. Although I works on my
local machine – a MBP running OSX 10.7 – but it never works on our web
server. It seems like it needs X11 display to be enabled to run. Is there a
way we can get around this?
Here is my java code for calling Jalview:
//run jalview to generate eps file
//basic command: java -Djava.ext.dirs=/Applications/Jalview/lib -cp
/Applications/Jalview/jalview.jar jalview.bin.Jalview -nodisplay -open
~/bin/ncbi-cobalt-2.0.1/col_fas.out -eps tmp2.eps
String jalview_input = outFile.getAbsolutePath();
String jalview_output = getTmpDir() + "/" +
uploadedFileNamePrefix + ".eps";
cmd = "java -Djava.ext.dirs=" + JALVIEW_BIN_PATH
+ "/lib -cp " +
JALVIEW_BIN_PATH + "/jalview.jar
jalview.bin.Jalview -nodisplay -open "+ jalview_input + " -eps " +
jalview_output;
System.out.println("###############Jalview CMD: "
+ cmd);
Process ls2_proc = Runtime.getRuntime().exec(cmd);
Worker worker = new Worker(ls2_proc);
worker.start();
worker.join(5000);
if (worker.exit == null){
worker.interrupt();
Thread.currentThread().interrupt();
ls2_proc.destroy();
}
Please note that I set up a timeout to kill the process because jalview
never exits after eps conversion is done.
I tried InstallAnywhere 2.8 release and development build.
Any help or suggestions will be appreciated.
By the way, if you are still looking for grant renew support letter I can
talk to my project manager to provide an official one.
Thanks,
Charlie Sun
--
Qiang(Charlie) Sun
Contractor - MSC, Inc.****
Senior Software Developer**
Bioinformatics Software Development Section****
Bioinformatics and Computational Biosciences Branch (BCBB)****
OCICB/OSMO/OD/NIAID/NIH****
****
31 Center Drive, Room 3B62****
Bethesda, MD 20892****
Mobile: 2404410620**
Office: 301-496-2498**
http://bioinformatics.niaid.nih.gov
http://bioinformatics.niaid.nih.gov/(Within NIH)****
http://exon.niaid.nih.gov (Public)
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