html link to load data

[laura.ve...@gmail.com]

Hi IGV,

I am trying to create a web page that would enable to load data in IGV, and am using html links to data to do so.

The three examples given in the user manual only enable to

1: load annotation files to an existing IGV genome (hg18 in this case)
http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&locus=egfr&genome=hg18

2: load a session file

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 IGV

http://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..)?

Many thanks,

Laura

[laura.ve...@gmail.com]

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,

[Jacob Silterra]

Are you trying to share a genome you create with others?

Something like this will allow loading a genome from any accessible URL:

http://localhost:60151/load?file=mydatafile.tdf&locus=egfr&genome=http://www.example.com/mygenome.genome

I can't access http://miseq.corpnet2.com/Yeast/, you need to make sure the computers on which this is run can access that URL.