ILRI Research Computing

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====== artic-tools ======
A set of tools for viral amplicon schemes:

  * download primer schemes and reference sequences
  * primer scheme validation
  * alignment softmasking
  * vcf filtering

===== Information =====

  * Version: 0.3.1
  * Added: February, 2023
  * Link: https://github.com/will-rowe/artic-tools

===== Usage =====

See which versions are available:
<code>$ module avail artic-tools</code>

Load one version into your environment and run it:
<code>$ module load artic-tools/0.3.1
$ artic-tools</code>


===== Installation ======
Notes from the sysadmin during installation.

<code>$ cd /tmp
$ git clone --recursive https://github.com/will-rowe/artic-tools.git
$ cd artic-tools
$ git checkout v0.3.1
$ module load htslib/1.15.1
$ mkdir build
$ cd build
$ cmake .. -DHTS_LIB=/export/apps/htslib/1.15.1/lib/libhts.so -DHTS_INCLUDE_DIR=/export/apps/htslib/1.15.1/include/ -DCMAKE_INSTALL_PREFIX=/export/apps/artic-tools/0.3.1
$ make -j4
$ make test
$ sudo mkdir -p /export/apps/artic-tools/0.3.1/bin                                                  
$ sudo cp ../bin/artic-tools /export/apps/artic-tools/0.3.1/bin</code>