Differences

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--- pilon-software [2018/11/18 06:50] – created aorth
+++ pilon-software [2025/05/06 07:38] (current) – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Version: 1.2.2
+  * Version: 1.24
   * Added: November, 2018
-  * Link:
+  * Updated: May, 2025
+  * Link: https://github.com/broadinstitute/pilon
 ===== Usage =====
-Pilon is distributed as a Java JAR file. You need to run it like this:
+See which versions are available:
-<code>$ java -Xmx16G -jar /export/apps/pilon/1.2.2/pilon-1.22.jar</code>
-The [[https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage|documentation recommends]] using a minimum of 8GB of memory, or 16GB if possible.
+<code>$ module avail pilon</code>
+Load one version into your environment and run it:
+<code>$ module load pilon/1.24
+$ pilon</code>
+Note: the [[https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage|documentation recommends]] using a minimum of 8GB of memory. As a rule of thumb, try to allocate 1GB of memory per megabase of input genome to be processed. To override the default memory allocation you will need to run Pilon directly, for example::
+<code>$ java -Xmx16G -jar /export/apps/pilon/1.24/pilon-1.24.jar</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>$ sudo mkdir -p /export/apps/pilon/1.2.2
+<code>$ sudo mkdir -p /export/apps/pilon/1.24
-$ sudo wget https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar -O /export/apps/pilon/1.2.2/pilon-1.22.jar</code>
+$ sudo wget https://github.com/broadinstitute/pilon/releases/download/v1.24/pilon-1.24.jar -O /export/apps/pilon/1.24/pilon-1.24.jar
+$ # edit /export/apps/pilon/1.24/pilon
+$ cat /export/apps/pilon/1.24/pilon
+#!/usr/bin/env bash
+readonly PREFIX=$(dirname $0)
+# Default to 8G of heap
+java -jar -Xmx8G $PREFIX/pilon-1.24.jar $*
+$ sudo chmod +x /export/apps/pilon/1.24/pilon</code>