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3. Running the Actual Assembly

.. docker::

   RUN apt-get -y install wget
   RUN pip install -U setuptools && pip install -U khmer==2.0

All of the below should be run in screen, probably... You will want at least 15 GB of RAM, maybe more.

(If you start up a new machine, you'll need to go to :doc:`1-quality` and go through the Install Software section.)

Note

You can start this tutorial with the contents of EC2/EBS snapshot snap-7b0b872e.

Installing Trinity

Flush the disk cache, then install trinity

To install Trinity:

cd ${HOME}

curl -L https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.3.2.tar.gz > trinity.tar.gz
tar xzf trinity.tar.gz
cd trinityrnaseq*/
make |& tee trinity-build.log

echo 9-compile-trinity DONE `date` >> ${HOME}/times.out

Assembling with Trinity

Run the assembler!

echo 10-big-assembly START `date` >> ${HOME}/times.out

${HOME}/trinity*/Trinity --left left.fq \
  --right right.fq --seqType fq --max_memory 14G \
  --CPU 2

echo 10-big-assembly DONE `date` >> ${HOME}/times.out

Note that this last two parts (--max_memory 14G --CPU ${THREADS:-2}) is the maximum amount of memory and CPUs to use. You can increase (or decrease) them based on what machine you rented. This size works for the m1.xlarge machines.

Once this completes (on the Nematostella data it might take about 12 hours), you'll have an assembled transcriptome in ${HOME}/projects/eelpond/trinity_out_dir/Trinity.fasta.

You can now copy it over via Dropbox, or set it up for BLAST (see :doc:`installing-blastkit`).