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--- htslib-software [2015/03/27 08:55] – created joguya
+++ htslib-software [2021/09/05 10:17] – aorth
@@ Line 1: / Line 1: @@
-====== 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 =====
-  * Version: 1.2.1
+  * Latest Version: 1.13
   * Added: March, 2015
+  * Updated: September, 2021
   * Link: https://github.com/samtools/htslib
 ===== Usage =====
-=== See versions of htslib which are available ===
+See versions of htslib which are available:
 <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/1.13
+$ tabix
+$ bgzip</code>
 ===== 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/1.13/htslib-1.13.tar.bz2
-tar -xvf 1.2.1.tar.gz
+$ tar xf htslib-1.13.tar.bz2
-cd htslib-1.2.1/
+$ cd htslib-1.13
-scl enable devtoolset-2 bash
+# install a newer compiler from Red Hat software collections
-sudo mkdir -p /export/apps/htslib/1.2.1
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
-sudo chown joguya:joguya /export/apps/htslib/1.2.1
+$ scl enable devtoolset-7 bash
-autoreconf
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/htslib/1.13
-./configure CC=clang --prefix=/export/apps/htslib/1.2.1
+$ make
-make
+$ sudo mkdir -p /export/apps/htslib/1.13
-make install
+$ sudo chown aorth /export/apps/htslib/1.13
-sudo chown root:root /export/apps/htslib/1.2.1
+$ make install
-</code>
+$ sudo chown -R root:root /export/apps/htslib/1.13</code>