artic-tools

A set of tools for viral amplicon schemes:

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

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

See which versions are available:

$ module avail artic-tools

Load one version into your environment and run it:

$ module load artic-tools/0.3.1
$ artic-tools

Notes from the sysadmin during installation.

$ 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