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samtools-software

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samtools-software [2017/06/30 15:02] – aorthsamtools-software [2021/09/05 10:32] – 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: 1.5+  * Latest Version: 1.13
   * Added: February, 2015   * Added: February, 2015
-  * Updated: June, 2017+  * Updated: September, 2021
   * Link: http://www.htslib.org   * Link: http://www.htslib.org
  
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 <code>$ module avail samtools</code> <code>$ module avail samtools</code>
  
-Load a particular version of samtools:+Load a particular version of samtools into your environment and run it:
  
-<code>$ module load samtools/1.5</code>+<code>$ module load samtools/1.13 
 +$ samtools</code>
  
 ===== Installation ===== ===== Installation =====
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 +$ wget https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2 
-$ tar xf samtools-1.5.tar.bz2 +$ tar xf samtools-1.13.tar.bz2 
-$ cd samtools-1.5 +$ cd samtools-1.13 
-$ scl enable devtoolset-4 bash +# install a newer compiler from Red Hat software collections 
-$ sudo mkdir /export/apps/samtools/1.5 +$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ 
-$ sudo chown aorth /export/apps/samtools/1.5 +$ scl enable devtoolset-7 bash 
-$ ./configure --enable-plugins --enable-libcurl --without-curses --prefix=/export/apps/samtools/1.5 +$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.13 --with-htslib=/export/apps/htslib/1.13 
-$ make all all-htslib +$ make 
-$ make install install-htslib +$ sudo mkdir -p /export/apps/samtools/1.13 
-$ sudo chown -R root:root /export/apps/samtools/1.5</code>+$ sudo chown aorth /export/apps/samtools/1.13 
 +$ make install 
 +$ sudo chown -R root:root /export/apps/samtools/1.13</code> 
 + 
 +This links against htslib/1.13, which is installed as a module.
samtools-software.txt · Last modified: 2022/06/23 09:35 by aorth