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samtools-software [2016/03/29 12:30] joguyasamtools-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.+  * Latest Version: 1.15.1
-  * Updated: March, 2016+
   * Added: February, 2015   * Added: February, 2015
-  * Link: http://www.htslib.org/+  * Updated: June, 2022 
 +  * 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</code>+$ samtools</code>
  
 ===== Installation ===== ===== Installation =====
 Notes from the sysadmin during 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/1.15.1/samtools-1.15.1.tar.bz2 
-cd samtools +tar xf samtools-1.15.1.tar.bz2 
-git checkout 1.2 +cd samtools-1.15.1 
-sudo mkdir -/export/apps/samtools/1.2/ +./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.15.1 --with-htslib=/export/apps/htslib/1.15.1
-$ sudo chown joguya:joguya /export/apps/samtools/1.2/+
 $ make $ make
-make prefix=/export/apps/samtools/1.2/ install +sudo mkdir -p /export/apps/samtools/1.15.1 
-$ sudo chown -R root:root /export/apps/samtools/1.2/</code>+$ sudo chown aorth /export/apps/samtools/1.15.1 
 +$ make install 
 +$ sudo chown -R root:root /export/apps/samtools/1.15.1</code> 
 + 
 +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.
samtools-software.1459254637.txt.gz · Last modified: 2016/03/29 12:30 by joguya