.. _Stacks:

Stacks
======

De acordo com a `página do Stacks <https://catchenlab.life.illinois.edu/stacks/>`_,
"*Stacks is a software pipeline for building loci from short-read sequences,
such as those generated on the Illumina platform. Stacks was developed to work
with restriction enzyme-based data, such as RAD-seq, for the purpose of
building genetic maps and conducting population genomics and phylogeography*".

Versões Disponíveis
-------------------

* stacks/2.4

Submissão de Jobs em Paralelo (SMP)
-----------------------------------

Crie um arquivo chamado, por exemplo, *submit_paral_jobs.sh*.

.. code-block:: bash

   #!/bin/bash
   #SBATCH -c 16
   
   module load stacks/2.4
   
   export INPUT="ustacks.sh *.fq.gz"
   export OUTPUT="*.tsv.gz"
   
   export LARGE_FILES="true"
   
   job-nanny ./ustacks.sh

em que o script *ustacks.sh* tem o seguinte conteúdo:

.. code-block:: bash

   ar=./
   file="90415
   90414
   90426
   90427
   90422
   90420
   "
   
   i=1
   for file in $file
   do
    ustacks -p 100 -t gzfastq -m 3 -M 4 -i $i \
               -f $ar/${file}.fq.gz  \
               -o $ar
    let "i+=1";
   done

Antes de submeter o job, deve-se tornar o script executável pelo comando

.. code-block:: bash

   chmod +x run.sh

Para submeter o processo, basta usar o comando:

.. code-block:: bash

   sbatch submit_paral_jobs.sh


Referências
-----------

Para informações adicionais sobre o software, consulte a `documentação do Stacks <https://catchenlab.life.illinois.edu/stacks/manual/>`_.