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samtools-software [2017/02/05 11:38] – joguyasamtools-software [2025/03/03 07:12] (current) – aorth
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 samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. 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: 1.3.1 +  * Latest Version: 1.17
-  * Updated: February, 2017+
   * Added: February, 2015   * Added: February, 2015
-  * Link: http://www.htslib.org/+  * 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> <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/1.3.1</code>+$ samtools</code>
  
 ===== Installation ===== ===== Installation =====
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code> +<code>$ cd /tmp 
-$ cd /tmp +$ wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 
-$ wget -qO- "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" | tar xjv +$ tar xf samtools-1.17.tar.bz2 
-$ cd samtools-1.3.1/ +$ cd samtools-1.17 
-$ scl enable devtoolset-2 bash +$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.17 --with-htslib=/export/apps/htslib/1.17 
-$ sudo mkdir /export/apps/samtools/1.3.1 +$ make 
-$ sudo chown -R joguya:joguya /export/apps/samtools/1.3.1 +$ sudo mkdir -p /export/apps/samtools/1.17 
-$ ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/htslib-1.3.1 --prefix=/export/apps/samtools/1.3.1 +$ sudo chown aorth /export/apps/samtools/1.17 
-$ make all install-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/1.3.1 + 
-</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.
samtools-software.1486294723.txt.gz · Last modified: 2017/02/05 11:38 by joguya