Question: IGV command line control
0
gravatar for damian.loska
2.3 years ago by
damian.loska10
damian.loska10 wrote:

Hi,

I know I can start IGV (Integrative Genomics Viewer, Broad Institute) providing some starting parameters (via specifying either a session file or a comma-delimited list of files to load), but is it possible somehow to control IGV from command line?

While IGV is running, I'd like to type in the terminal for example "goto chr1:65,839,697" and without closing current session and opening a new session it would go to this location.

Thanks! Damian

igv control remote command line • 3.4k views
ADD COMMENTlink modified 2.3 years ago by dariober11k • written 2.3 years ago by damian.loska10

Have you seen these?

http://software.broadinstitute.org/software/igv/PortCommands

http://software.broadinstitute.org/software/igv/batch

ADD REPLYlink written 2.3 years ago by Dan D7.1k

Yes, I've seen this, but as I understand it works only when I start a new session. I'd like to have a solution to interact with an active session, not via "Tools>Run Batch Script", but through command line.

ADD REPLYlink written 2.3 years ago by damian.loska10

You might want to try using the load 'file' command listed there to try and load a previously saved session .xml file or similar.

ADD REPLYlink written 2.3 years ago by steve2.5k
1
gravatar for damian.loska
2.3 years ago by
damian.loska10
damian.loska10 wrote:

Ok I've solved it! I wanted to send command via my webpage. This is the example solution:

<A href='http://localhost:60151/goto?locus=Ch1:100000'>link</A>

(I thought that firstly I'd need to create some "command file", then run it via terminal to obtain the effect. The solution was much simpler for my needs)

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by damian.loska10
1
gravatar for Pierre Lindenbaum
2.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

an old post : http://plindenbaum.blogspot.fr/2011/07/controlling-igv-through-port-my.html

Controlling IGV through a Port: my notebook.

Via a shell script

$ cat script.sh

mkdir -p /tmp/igv
sleep 2
echo "snapshotDirectory /tmp/igv"
sleep 2
echo "goto chr3:100"
sleep 2
echo "snapshot"
sleep 2
echo "goto chr3:200-300"
sleep 2
echo "snapshot"
sleep 2

invoke the script with telnet

$ sh script.sh |  telnet 127.0.0.1 60151
Trying 127.0.0.1...
Connected to srv-clc-02.irt.univ-nantes.prive (127.0.0.1).
Escape character is '^]'.
INFO [2011-07-27 17:58:16,680]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:18,685]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:18,687]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_80_119.png
INFO [2011-07-27 17:58:20,787]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:22,792]  [CommandExecutor.java:124] [Thread-6]  OK
OK
INFO [2011-07-27 17:58:22,794]  [MacroSnapshotAction.java:85] [Thread-6]  Snapshot: chr3_200_300.png
Connection closed by foreign host.
ADD COMMENTlink written 2.3 years ago by Pierre Lindenbaum128k
0
gravatar for andrew.j.skelton73
2.3 years ago by
London
andrew.j.skelton735.9k wrote:

While I've not seen any specific CLI for IGV control, one of the more useful tools I found (that you may be trying to achieve overall...), is IGV Screenshot.

ADD COMMENTlink written 2.3 years ago by andrew.j.skelton735.9k

similar tools implemented in python here: https://github.com/stevekm/IGV-snapshot-automator

ADD REPLYlink written 2.3 years ago by steve2.5k
0
gravatar for dariober
2.3 years ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

I've been wondering about this question in the past and I ended up writing my own tool to browse the genome from the command line, ASCIIGenome. Feel free to give it a try and post issues here or on the github repository.

ADD COMMENTlink written 2.3 years ago by dariober11k
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