stevekm · August 21, 2025 16:51 · Nov 2, 2016 · Nov 2, 2016 · Nov 2, 2016 · Nov 2, 2016
diff --git a/igv_test_bat.md b/igv_test_bat.md
@@ -48,7 +48,15 @@ For scripting purposes, you can run the X11 virtualizer to avoid the requirement
 (Xvfb :10 &) && DISPLAY=:10 java -Xmx750m -jar bin/IGV_2.3.81/igv.jar -b code/IGV_test.bat && killall Xvfb
 ```
 
-Note that you can run an IGV batch script from within IGV itself as well. This allows you to load your tracks and apply manual customization, then iterate through a series of regions and take snapshots. 
+Note that you can run an IGV batch script from within IGV itself as well. This allows you to load your tracks and apply manual customization, then iterate through a series of regions and take snapshots. Just omit the portions of the script that start and new session & adjust visual parameters. If you've already loaded your tracks, all your script needs is this:
+
+```
+snapshotDirectory /path/to/snapshot_dir
+goto chr11:108138003-108138003
+snapshot custom_chr11-108138003-108138003.png
+goto chr9:21971111-21971111
+snapshot custom_chr9-21971111-21971111.png
+```
 
 Example output:
 

diff --git a/igv_test_bat.md b/igv_test_bat.md
@@ -1,3 +1,5 @@
+You can use IGV to automatically & programmatically load genomic datasets and take snapshots of regions of interest. This is very handy and helps you avoid taking many screenshots manually. 
+
 Manual page here:
 
 http://software.broadinstitute.org/software/igv/batch
@@ -10,7 +12,7 @@ Download here:
 
 http://software.broadinstitute.org/software/igv/download
 
-After installing IGV, a script can be run from the terminal. Sample script (save this as `IGV_test.bat`):
+After installing IGV, a specially-formatted IGV batch script can be used to automate the program. Format your script like this: (save this as `IGV_test.bat`):
 
 ```
 new
@@ -26,13 +28,13 @@ snapshot custom_chr9-21971111-21971111.png
 exit
 ```
 
-Example command to run IGV:
+You can run the script from the terminal like this:
 
 ```
 bin/IGV_2.3.81/igv.sh -b code/IGV_test.bat
 ```
 
-Running the script like this will cause a window to appear, and the commands will be executed.
+Upon running the script, a window to appear and you should see the tracks load and the regions appear on screen as snapshots are taken.
 
 If you are running IGV from a headless server (accessing the server via `ssh`), then this will require X11 to be running on the server and installed on your local computer (use XQuartz for OS X). Remember to enable X11 in your terminal by adding `-Y` to your `ssh` command, like so:
 

diff --git a/igv_test_bat.md b/igv_test_bat.md
@@ -46,6 +46,8 @@ For scripting purposes, you can run the X11 virtualizer to avoid the requirement
 (Xvfb :10 &) && DISPLAY=:10 java -Xmx750m -jar bin/IGV_2.3.81/igv.jar -b code/IGV_test.bat && killall Xvfb
 ```
 
+Note that you can run an IGV batch script from within IGV itself as well. This allows you to load your tracks and apply manual customization, then iterate through a series of regions and take snapshots. 
+
 Example output:
 
 ![chr3_185850354-185872709](https://cloud.githubusercontent.com/assets/10505524/19937792/013ef1d8-a0f9-11e6-8b17-289de9706c1d.png)
diff --git a/igv_test_bat.md b/igv_test_bat.md
@@ -44,4 +44,8 @@ For scripting purposes, you can run the X11 virtualizer to avoid the requirement
 
 ```
 (Xvfb :10 &) && DISPLAY=:10 java -Xmx750m -jar bin/IGV_2.3.81/igv.jar -b code/IGV_test.bat && killall Xvfb
-```
+```
+
+Example output:
+
+![chr3_185850354-185872709](https://cloud.githubusercontent.com/assets/10505524/19937792/013ef1d8-a0f9-11e6-8b17-289de9706c1d.png)
diff --git a/igv_test_bat.md b/igv_test_bat.md
@@ -6,6 +6,9 @@ These commands are also available:
 
 http://software.broadinstitute.org/software/igv/PortCommands
 
+Download here:
+
+http://software.broadinstitute.org/software/igv/download
 
 After installing IGV, a script can be run from the terminal. Sample script (save this as `IGV_test.bat`):
 
@@ -28,3 +31,17 @@ Example command to run IGV:
 ```
 bin/IGV_2.3.81/igv.sh -b code/IGV_test.bat
 ```
+
+Running the script like this will cause a window to appear, and the commands will be executed.
+
+If you are running IGV from a headless server (accessing the server via `ssh`), then this will require X11 to be running on the server and installed on your local computer (use XQuartz for OS X). Remember to enable X11 in your terminal by adding `-Y` to your `ssh` command, like so:
+
+```
+ssh [email protected] -Y
+```
+
+For scripting purposes, you can run the X11 virtualizer to avoid the requirement for an active X11 window when you call IGV. Use this command:
+
+```
+(Xvfb :10 &) && DISPLAY=:10 java -Xmx750m -jar bin/IGV_2.3.81/igv.jar -b code/IGV_test.bat && killall Xvfb
+```
diff --git a/igv_test_bat.md b/igv_test_bat.md
@@ -1,5 +1,13 @@
+Manual page here:
 
-Save this as a test file
+http://software.broadinstitute.org/software/igv/batch
+
+These commands are also available:
+
+http://software.broadinstitute.org/software/igv/PortCommands
+
+
+After installing IGV, a script can be run from the terminal. Sample script (save this as `IGV_test.bat`):
 
 ```
 new
@@ -13,4 +21,10 @@ snapshot custom_chr11-108138003-108138003.png
 goto chr9:21971111-21971111
 snapshot custom_chr9-21971111-21971111.png
 exit
-```
+```
+
+Example command to run IGV:
+
+```
+bin/IGV_2.3.81/igv.sh -b code/IGV_test.bat
+```
diff --git a/igv_test_bat.md b/igv_test_bat.md
@@ -0,0 +1,16 @@
+
+Save this as a test file
+
+```
+new
+snapshotDirectory /path/to/snapshot_dir
+load /path/to/sample1.bam
+load /path/to/sample2.bam
+genome hg19
+maxPanelHeight 400
+goto chr11:108138003-108138003
+snapshot custom_chr11-108138003-108138003.png
+goto chr9:21971111-21971111
+snapshot custom_chr9-21971111-21971111.png
+exit
+```