http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/exampleFiles/gbm_session.xml&merge=true
3: Jump to a locus in a genome already loaded in IGVhttp://localhost:60151/goto?locus=egfr
Is it possible to directly load my own genome file from URL (command 'load?genome' or something of the sort..)?Hi IGV,
Let me give more details...
I am trying to create my genome server.
I have followed all the steps mentioned in: http://www.broadinstitute.org/software/igv/configuring_genome_server
But I still get this error.
miseq> ./igv.sh
INFO [2013-05-14] [DirectoryManager.java:149] [main] IGV Directory: /home/lv155535/igv
INFO [2013-05-14] [Main.java:72] [main] Startup IGV Version 2.2.10 (13)03/11/2013 12:06 AM
INFO [2013-05-14] [Main.java:73] [main] Java 1.7.0_17
Fetching user directory... INFO [2013-05-14] [Main.java:74] [main] Default User Directory: /home/lv155535
INFO [2013-05-14] [CommandListener.java:80] [Thread-6] Listening on port 60151
INFO [2013-05-14] [GenomeManager.java:113] [pool-1-thread-1] Loading genome: http://miseq.corpnet2.com/Yeast.genome
ERROR [2013-05-14] [IGVCommandBar.java:264] [pool-1-thread-1] Error initializing genome
java.lang.NullPointerException
at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:258)
at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:124)
at org.broad.igv.ui.IGVCommandBar$4.run(IGVCommandBar.java:231)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:54)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)
My property.txt file contains:
fasta=true
fastaDirectory=false
ordered=true
id=Yeast
name=Yeast
sequenceLocation=http://miseq.corpnet2.com/Yeast/
and this web accessible directory http://miseq.corpnet2.com/Yeast/ contains the fasta sequence of a yeast chromosome.
When I create a .genome file of my genome I only get the file and no associated directory. I have just created one containing the fasta sequence and placed in a web accessible location. Is that correct?
Many thanks in advance for your help,