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samtools-software [2017/06/30 14:40] aorthsamtools-software [2022/06/23 09:35] (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: 1.15.1
   * Added: February, 2015   * Added: February, 2015
-  * Updated: February2017+  * Updated: June2022
   * Link: http://www.htslib.org   * 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/1.15.1 
-<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/1.15.1/samtools-1.15.1.tar.bz2 
-$ wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 +$ tar xf samtools-1.15.1.tar.bz2 
-$ tar xf samtools-1.3.1.tar.bz2 +$ cd samtools-1.15.1 
-$ cd samtools-1.3.1/ +./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.15.1 --with-htslib=/export/apps/htslib/1.15.1 
-scl enable devtoolset-2 bash +make 
-$ sudo mkdir /export/apps/samtools/1.3.1 +sudo mkdir -p /export/apps/samtools/1.15.1 
-$ sudo chown -R joguya:joguya /export/apps/samtools/1.3.1 +$ sudo chown aorth /export/apps/samtools/1.15.1 
-./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/htslib-1.3.1 --prefix=/export/apps/samtools/1.3.1 +$ make install 
-$ make all install-htslib +$ sudo chown -R root:root /export/apps/samtools/1.15.1</code> 
-$ make install install-htslib + 
-$ sudo chown -R root:root /export/apps/samtools/1.3.1 +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.
-</code>+
samtools-software.txt · Last modified: 2022/06/23 09:35 by aorth