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samtools-software [2021/09/05 10:32] – aorthsamtools-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: 1.13+  * Latest Version: 1.17
   * Added: February, 2015   * Added: February, 2015
-  * Updated: September, 2021+  * Updated: March, 2025
   * 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 into your environment and run it: +Load one version into your environment and run it: 
- +<code>$ module load samtools/1.17
-<code>$ module load samtools/1.13+
 $ samtools</code> $ samtools</code>
  
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2 +$ wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 
-$ tar xf samtools-1.13.tar.bz2 +$ tar xf samtools-1.17.tar.bz2 
-$ cd samtools-1.13 +$ cd samtools-1.17 
-# install a newer compiler from Red Hat software collections +$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.17 --with-htslib=/export/apps/htslib/1.17
-$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ +
-$ scl enable devtoolset-7 bash +
-$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.13 --with-htslib=/export/apps/htslib/1.13+
 $ make $ make
-$ sudo mkdir -p /export/apps/samtools/1.13 +$ sudo mkdir -p /export/apps/samtools/1.17 
-$ sudo chown aorth /export/apps/samtools/1.13+$ sudo chown aorth /export/apps/samtools/1.17
 $ make install $ make install
-$ sudo chown -R root:root /export/apps/samtools/1.13</code>+$ sudo chown -R root:root /export/apps/samtools/1.17</code>
  
-This links against htslib/1.13, which is installed as a module.+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.1630837920.txt.gz · Last modified: 2021/09/05 10:32 by aorth