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htslib-software [2015/03/27 08:55]
joguya created 		htslib-software [2021/01/06 09:16] (current)
aorth
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-====== HTSlib ====== +====== htslib ====== 
-HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools+htslib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools
  
 ===== Information ===== ===== Information =====
  
-  * Version: 1.2.1+  * Latest Version: 1.11
   * Added: March, 2015   * Added: March, 2015
 +  * Updated: January, 2021
   * Link: https://github.com/samtools/htslib   * Link: https://github.com/samtools/htslib
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of htslib which are available ===+See versions of htslib which are available:
 <code>$ module avail htslib</code> <code>$ module avail htslib</code>
  
-=== Load and run htslib === +Load one version into your environment and run some common commands: 
-<code>$ module load htslib </code>+<code>$ module load htslib/1.11 
 +$ tabix 
 +$ bgzip</code>
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>cd /tmp +<code>$ cd /tmp/ 
-wget https://github.com/samtools/htslib/archive/1.2.1.tar.gz +$ wget https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2 
-tar -xvf 1.2.1.tar.gz +$ tar xf htslib-1.11.tar.bz2 
-cd htslib-1.2.1/ +$ cd htslib-1.11 
-scl enable devtoolset-2 bash +$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/htslib/1.11 
-sudo mkdir -p /export/apps/htslib/1.2.1 +$ make 
-sudo chown joguya:joguya /export/apps/htslib/1.2.1 +$ sudo mkdir -p /export/apps/htslib/1.11 
-autoreconf +$ sudo chown aorth /export/apps/htslib/1.11 
-./configure CC=clang --prefix=/export/apps/htslib/1.2.1 +$ make install 
-make +$ sudo chown -R root:root /export/apps/htslib/1.11</code>
-make install +
-sudo chown root:root /export/apps/htslib/1.2.1 +
-</code>+
htslib-software.1427446501.txt.gz · Last modified: 2015/03/27 08:55 by joguya

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