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bcftools-software [2017/02/05 11:42]
joguya [Installation]
bcftools-software [2021/09/05 10:51] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Latest Version: 1.3.1+  * Latest Version: 1.13
   * Added: September, 2015   * Added: September, 2015
-  * Updated: February2017+  * Updated: September2021
   * Link: https://samtools.github.io/bcftools   * Link: https://samtools.github.io/bcftools
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of bcftools which are available ===+See versions of bcftools which are available:
 <code>$ module avail bcftools</code> <code>$ module avail bcftools</code>
 +
 +Load one version into your environment and run it:
 +<code>$ module load bcftools/1.13
 +$ bcftools</code>
  
 ===== Installation ====== ===== Installation ======
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget -qO- https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 | tar xjv +$ wget https://github.com/samtools/bcftools/releases/download/1.13/bcftools-1.13.tar.bz2 
-$ cd bcftools-1.3.1 +$ tar xf bcftools-1.13.tar.bz2  
-$ scl enable devtoolset-bash +$ cd bcftools-1.13 
-sudo mkdir /export/apps/bcftools/1.3.1 +# install a newer compiler from Red Hat software collections 
-$ HTSDIR=/export/apps/htslib/1.3.2 make +$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ 
-$ make prefix=/export/apps/bcftools/1.3.install +$ scl enable devtoolset-bash 
-$ sudo chown -R root:root /export/apps/bcftools/1.3.1 +./configure --enable-plugins --enable-libcurl --prefix=/export/apps/bcftools/1.13 --with-htslib=/export/apps/htslib/1.13 
-</code>+$ make 
 +$ sudo mkdir -p /export/apps/bcftools/1.13 
 +$ sudo chown aorth /export/apps/bcftools/1.13 
 +make install 
 +sudo chown -R root:root /export/apps/bcftools/1.13</code> 
 + 
 +This links bcftools against a system-wide installation of htslib/1.13.
bcftools-software.1486294938.txt.gz · Last modified: 2017/02/05 11:42 by joguya