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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 and run htslib

$ module load htslib/1.3.2 

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget -qO- "https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2" | tar xjv
$ sudo mkdir /export/apps/htslib/1.3.2/
$ sudo chown -R joguya:joguya /export/apps/htslib/1.3.2/
$ LD_LIBRARY_PATH=/export/apps/curl/7.47.1/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/curl/7.47.1/lib" CFLAGS="-I/export/apps/curl/7.47.1/include" ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/htslib/1.3.2/
$ make
$ make install
$ sudo chown -R root:root /export/apps/htslib/1.3.2
htslib-software.txt · Last modified: 2017/05/04 12:20 by aorth