Differences

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--- samtools-software [2015/06/09 16:40] – aorth
+++ samtools-software [2025/03/03 07:12] (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.
-  * Version: 1.2
+  * Latest Version: 1.17
   * Added: February, 2015
-  * Link: http://samtools.sourceforge.net/
+  * Updated: March, 2025
+  * Link: http://www.htslib.org
-=== Usage ===
+===== 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/1.17
+$ samtools</code>
-<code>$ module load samtools/1.2</code>
+===== Installation =====
-=== Installation ===
 Notes from the sysadmin during installation:
-<code>$ git clone git@github.com:samtools/htslib.git
+<code>$ cd /tmp
-$ git clone git@github.com:samtools/samtools.git
+$ wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
-$ cd samtools
+$ tar xf samtools-1.17.tar.bz2
-$ git checkout 1.2
+$ cd samtools-1.17
-$ sudo mkdir -p /export/apps/samtools/1.2/
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.17 --with-htslib=/export/apps/htslib/1.17
-$ sudo chown joguya:joguya /export/apps/samtools/1.2/
 $ make
-$ make prefix=/export/apps/samtools/1.2/ install
+$ sudo mkdir -p /export/apps/samtools/1.17
-$ sudo chown -R root:root /export/apps/samtools/1.2/</code>
+$ sudo chown aorth /export/apps/samtools/1.17
+$ make install
+$ sudo chown -R root:root /export/apps/samtools/1.17</code>
+Note: this links against htslib/1.17, which is installed as a module. As of 1.17 this was compiled on CentOS 8 Stream.