install silently on multiple computers

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grant little

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Jul 19, 2016, 1:10:21 PM7/19/16
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Hello,
I'd like toi install IGV on multiple computers to use for teaching in a class.
Is there a way to install silently, that is, suppress dialogs during installation?
Also is there an easy way to register multiple emails for use with IGV?

Thanks for your help.

Jim Robinson

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Jul 20, 2016, 2:04:04 PM7/20/16
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Hi,

We don't have a script for doing that, but if you could describe your environment I could provide some suggestions (windows, mac, linux)?

We usually ask students to do this themselves, its the "first lesson".

Jim

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grant little

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Jul 21, 2016, 11:48:00 AM7/21/16
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Thanks Jim. Apologies for not previously describing the environment.
Two labs with  24 computers in each, running windows 7, 64-bit.
So far I have figured out that I can run the installer  on a single system and then copy the IGV_2.3.79_jre folder to the target computers at say c:\IGV_2.3.79_jre and create a start menu shortcut that starts from that folder.

We have our computers setup to use shared drive space for their user data and the log shows that IGV recognizes that:
"INFO [2016-07-20 12:51:10,455] [Main.java:99] Startup IGV Version 2.3.79 (118)07/09/2016 11:48 PM
INFO [2016-07-20 12:51:10,455] [Main.java:100] Java 1.8.0_91
INFO [2016-07-20 12:51:10,456] [Main.java:101] Default User Directory: \\myuniversity.edu\CifsHome\115\<username>

but then IGV uses the USERPROFILE to look for (and store) the IGV profile:

INFO [2016-07-20 12:51:10,456] [Main.java:102] OS: Windows 7
INFO [2016-07-20 12:51:19,913] [GenomeManager.java:1017] java.io.FileNotFoundException: C:\Users\<username>\igv\genomes\user-defined-genomes.txt (The system cannot find the file specified)

Our systems are setup so that not all the user profile data is saved between sessions. Instead user data is stored in the default user directory. As a result students would need to setup IGV every time they used it.
We can't afford the drive space to store complete applications in the Default User Directory but a few settings is fine.

So I guess my question now changes to: with IGV installed in a common location, how to start IGV with it reading and saving the user profile from/to the Default User Directory?  
I will try using  -o <file> in the shortcut that starts IGV as mentioned here: https://www.broadinstitute.org/software/igv/startingIGV

I am also keen to learn how you would approach this for our systems.

Thanks.

grant little

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Jul 21, 2016, 1:04:37 PM7/21/16
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OK I changed the shortcut to 
C:\IGV_2.3.79_jre\igv.bat -o %HOMESHARE%\igv

and it seems to work just fine.
Thanks.
Message has been deleted

grant little

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Jul 21, 2016, 2:09:10 PM7/21/16
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I spoke too soon. I was watching the startup in the DOS window and I could see the -o directive working . However although it is accepting the -o parameter it appears to not use the path.
I'm still stuck on how to make IGV start using a different path for preferences and saving genomes. 

On Thursday, July 21, 2016 at 11:05:50 AM UTC-7, grant little wrote:

Jim Robinson

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Jul 21, 2016, 7:00:26 PM7/21/16
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OK, I can give you a couple of things to try. I'm somewhat hampered
here because I'm traveling and answering emails in airports.

The igv directory path is stored in Java preferences under the key
"igvDir". I don't really know where Java stores preferences on
Windows, probably in the registry, but you could try setting that.
However, if everyone is running as the same user that probably wouldn't
work.

I have added a command line override to set the path on startup, the key
is --igvDirectory. This was in response to another ticket, and it
hasn't been tested thoroughly or released yet. It is in the
development build, available here:
http://www.broadinstitute.org/igv/projects/downloads/snapshot/IGV_Snapshot.zip.
To use this with your current setup unzip the archive, then replace
"igv.jar" in the lib folder with the new one. I tested the snapshot
with the following command line (on my Mac).

java -Xmx4000m -jar igv.jar --igvDirectory /Users/jrobinso/TEST/IGV/

This will be released with 2.3.80 by the end of the month.

Jim

grant little

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Jul 22, 2016, 11:15:45 AM7/22/16
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Thank you for taking the time to respond when on the road.
I can't find any igvDir setting in the registry but there is an entry for igv in the user prefs at HKEY_CURRENT_USER\Software\JavaSoft\Prefs\org\broad\igv
but it is empty
There's a bunch of Java settings at HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\JavaSoft but nothing related to igv as far as I can tell.

Your snapshot works well IFF the /user/.../igv directory is already created. However if it is not there already it does not get created, instead it defaults to and creates /Users/<username>/igv
Thre snapshot is very promising and I look forward to the release version at the end of the month. Thanks! Much appreciated.

Jim Robinson

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Jul 22, 2016, 11:47:08 AM7/22/16
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OK, thanks for trying it.   I will open an issue to try to create the directory if it doesn't exist,  however this might fail for a variety of reasons.   So its best to create the directory first.

RE the Java settings,  you will only find an entry if you have changed the user directory from the Preferences UI window.   Sorry I should have mentioned that.   However, I think its safer to use the new command line option,  where Java store preferences is not documented and they could change that,  thought probably not during the time period of your course.

Its perfectly o.k. to use the snapshot jar in your situation if you need it prior to release.

Jim

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grant little

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Jul 25, 2016, 10:16:28 AM7/25/16
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Thanks. Creating the directory in advance is not an easy option as the users are not easily known in advance, so I look forward to the new release or prototype implementing that feature.
OTOH I guess I could create a script that did that as part of the IGV startup, and then use your existing snapshot.
I'll also try the registry approach 

grant little

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Jul 25, 2016, 10:57:45 AM7/25/16
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I've gone with creating the directory from the batch file that starts IGV using

mkdir %HOMESHARE%\IGV > NUL

and along with your snapshot that works great so I have a working solution now and due to pressure of other work won't be testing the registry approach .
Thanks for your help. Really appreciated.

For other readers here's the whole batch file, note it uses the snapshot:

:: create IGV dir in users share. This does not overwrite any existing dir
mkdir %HOMESHARE%\IGV > NUL
::Get the current batch file's short path
for %%x in (%0) do set BatchPath=%%~dpsx
for %%x in (%BatchPath%) do set BatchPath=%%~dpsx
java -Xmx4000m -Djava.net.preferIPv4Stack=true -Dsun.java2d.noddraw=true -jar igv.jar --igvDirectory %HOMESHARE%\IGV
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