Differences

This shows you the differences between two versions of the page.

--- samtools-software [2018/06/01 19:31] – aorth
+++ samtools-software [2022/06/23 09:35] (current) – aorth
@@ Line 2: / Line 2: @@
 samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-  * Latest Version: 1.8
+  * Latest Version: 1.15.1
   * Added: February, 2015
-  * Updated: June, 2018
+  * Updated: June, 2022
   * Link: http://www.htslib.org
 ===== Usage =====
-Show all available versions of samtools:
+Show all available versions:
 <code>$ module avail samtools</code>
-Load a particular version of samtools:
+Load one version into your environment and run it:
+<code>$ module load samtools/1.15.1
-<code>$ module load samtools/1.8</code>
+$ samtools</code>
 ===== Installation =====
@@ Line 20: / Line 20: @@
 <code>$ cd /tmp
-$ wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2
+$ wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
-$ tar xf samtools-1.8.tar.bz2
+$ tar xf samtools-1.15.1.tar.bz2
-$ cd samtools-1.8
+$ cd samtools-1.15.1
-$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.8 --with-htslib=/export/apps/htslib/1.8
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.15.1 --with-htslib=/export/apps/htslib/1.15.1
 $ make
-$ sudo mkdir /export/apps/samtools/1.8
+$ sudo mkdir -p /export/apps/samtools/1.15.1
-$ sudo chown aorth:aorth /export/apps/samtools/1.8
+$ sudo chown aorth /export/apps/samtools/1.15.1
 $ make install
-$ sudo chown -R root:root /export/apps/samtools/1.8</code>
+$ sudo chown -R root:root /export/apps/samtools/1.15.1</code>
-This links against a system-wide version of htslib/1.8.
+This links against htslib/1.15.1, which is installed as a module. As of 1.15.1 this was compiled on CentOS 8 Stream.