Differences

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--- samtools-software [2017/06/30 15:02] – 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.
-  * Latest Version: 1.5
+  * Latest Version: 1.17
   * Added: February, 2015
-  * Updated: June, 2017
+  * Updated: March, 2025
   * 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/1.17
-<code>$ module load samtools/1.5</code>
+$ samtools</code>
 ===== Installation =====
@@ Line 20: / Line 20: @@
 <code>$ cd /tmp
-$ wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2
+$ wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
-$ tar xf samtools-1.5.tar.bz2
+$ tar xf samtools-1.17.tar.bz2
-$ cd samtools-1.5
+$ cd samtools-1.17
-$ scl enable devtoolset-4 bash
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.17 --with-htslib=/export/apps/htslib/1.17
-$ sudo mkdir /export/apps/samtools/1.5
+$ make
-$ sudo chown aorth /export/apps/samtools/1.5
+$ sudo mkdir -p /export/apps/samtools/1.17
-$ ./configure --enable-plugins --enable-libcurl --without-curses --prefix=/export/apps/samtools/1.5
+$ sudo chown aorth /export/apps/samtools/1.17
-$ make all all-htslib
+$ make install
-$ make install install-htslib
+$ sudo chown -R root:root /export/apps/samtools/1.17</code>
-$ sudo chown -R root:root /export/apps/samtools/1.5</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.