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htslib-software

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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

Information

Usage

See versions of htslib which are available:

$ module avail htslib

Load one version into your environment and run some common commands:

$ module load htslib/1.9
$ tabix
$ bgzip

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
$ tar xf htslib-1.9.tar.bz2
$ cd htslib-1.9
# 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/htslib/1.9
$ make
$ sudo mkdir -p /export/apps/htslib/1.9
$ sudo chown aorth /export/apps/htslib/1.9
$ make install
$ sudo chown -R root:root /export/apps/htslib/1.9
htslib-software.txt · Last modified: 2019/09/04 00:47 by aorth