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samtools-software [2017/12/24 17:38]
aorth
samtools-software [2018/06/01 22:31] (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: 1.6+  * Latest Version: 1.8
   * Added: February, 2015   * Added: February, 2015
-  * Updated: ​December2017+  * Updated: ​June2018
   * Link: http://​www.htslib.org   * Link: http://​www.htslib.org
  
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 Load a particular version of samtools: Load a particular version of samtools:
  
-<​code>​$ module load samtools/1.6</​code>​+<​code>​$ module load samtools/1.8</​code>​
  
 ===== Installation ===== ===== Installation =====
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 <​code>​$ cd /tmp <​code>​$ cd /tmp
-$ wget https://​github.com/​samtools/​samtools/​releases/​download/​1.6/​samtools-1.6.tar.bz2 +$ wget https://​github.com/​samtools/​samtools/​releases/​download/​1.8/​samtools-1.8.tar.bz2 
-$ tar xf samtools-1.6.tar.bz2  +$ tar xf samtools-1.8.tar.bz2  
-$ cd samtools-1.6 +$ cd samtools-1.8 
-$ ./configure --enable-plugins --enable-libcurl --prefix=/​export/​apps/​samtools/​1.6 +$ ./configure --enable-plugins --enable-libcurl --prefix=/​export/​apps/​samtools/​1.8 --with-htslib=/​export/​apps/​htslib/​1.8 
-$ make all all-htslib +$ make 
-$ sudo mkdir /​export/​apps/​samtools/​1.6 +$ sudo mkdir /​export/​apps/​samtools/​1.8 
-$ sudo chown aorth /​export/​apps/​samtools/​1.6 +$ sudo chown aorth:aorth /​export/​apps/​samtools/​1.8 
-$ make install ​install-htslib +$ make install 
-$ sudo chown -R root:root /​export/​apps/​samtools/​1.6</​code>​+$ sudo chown -R root:root /​export/​apps/​samtools/​1.8</​code>​ 
 + 
 +This links against a system-wide version of htslib/1.8.
samtools-software.txt · Last modified: 2018/06/01 22:31 by aorth