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samtools-software [2018/06/01 22:31]
aorth
samtools-software [2019/09/04 01:00] (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: 1.8+  * Latest Version: 1.9
   * Added: February, 2015   * Added: February, 2015
-  * Updated: ​June2018+  * Updated: ​September2019
   * 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/1.8</​code>​+<​code>​$ module load samtools/1.9</​code>​
  
 ===== Installation ===== ===== Installation =====
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 <​code>​$ cd /tmp <​code>​$ cd /tmp
-$ wget https://​github.com/​samtools/​samtools/​releases/​download/​1.8/​samtools-1.8.tar.bz2 +$ wget https://​github.com/​samtools/​samtools/​releases/​download/​1.9/​samtools-1.9.tar.bz2 
-$ tar xf samtools-1.8.tar.bz2  +$ tar xf samtools-1.9.tar.bz2 
-$ cd samtools-1.8 +$ cd samtools-1.
-$ ./configure --enable-plugins --enable-libcurl --prefix=/​export/​apps/​samtools/​1.--with-htslib=/​export/​apps/​htslib/​1.8+# install a newer compiler from Red Hat software collections 
 +$ 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.--with-htslib=/​export/​apps/​htslib/​1.9
 $ make $ make
-$ sudo mkdir /​export/​apps/​samtools/​1.8 +$ sudo mkdir -p /​export/​apps/​samtools/​1.9 
-$ sudo chown aorth:aorth /​export/​apps/​samtools/​1.8+$ sudo chown aorth /​export/​apps/​samtools/​1.9
 $ make install $ make install
-$ sudo chown -R root:root /​export/​apps/​samtools/​1.8</​code>​+$ sudo chown -R root:root /​export/​apps/​samtools/​1.9</​code>​
  
-This links against a system-wide version of htslib/1.8.+This links against ​htslib installed as module in htslib/1.9.
samtools-software.txt · Last modified: 2019/09/04 01:00 by aorth