Install PacBio SMRTLink on AWS instance

installsmrtlink.md

How to install PacBio SMRTLink on an AWS instance

Launch and config an EC2 instance

m3.2xlarge (8 CPUs, X GB ram, 2 x 80GB SSD instance storage)

Copy your data files to the instance

scp -r -i aws.pem data_files ec2-user@54.89.153.29:
#ok to leave in the ec2-user home dir for now 

Install SMRTLink

First, download and unzip it

curl -O https://downloads.pacbcloud.com/public/software/installers/smrtlink_4.0.0.190159.zip
unzip -P SmrT3chN smrtlink_4.0.0.190159.zip

Now you can install it right here (doesn't matter where)

smrtlink_4.0.0.190159.run --rootDir smrtlink 

You will need to provide all the options. Most (all?) can be left as default.

Run the consensus with barcoding

You can use the provided preset.xml (in this gist) and sub.sh in this gist

preset.xml

<?xml version="1.0" encoding="utf-8" ?>
<pipeline-preset-template>
    <options>
        <option id="pbsmrtpipe.options.debug_mode">
            <value>False</value>
        </option>
        <option id="pbsmrtpipe.options.max_nproc">
            <value>8</value>
        </option>
        <option id="pbsmrtpipe.options.tmp_dir">
            <value>/tmp</value>
        </option>
        <option id="pbsmrtpipe.options.chunk_mode">
            <value>False</value>
        </option>
        <option id="pbsmrtpipe.options.max_nchunks">
            <value>1</value>
        </option>
        <option id="pbsmrtpipe.options.distributed_mode">
            <value>False</value>
        </option>
        <option id="pbsmrtpipe.options.exit_on_failure">
            <value>False</value>
        </option>
        <option id="pbsmrtpipe.options.cluster_manager">
            <value></value>
        </option>
        <option id="pbsmrtpipe.options.max_nworkers">
            <value>100</value>
        </option>
    </options>
    <task-options>
        <option id="pbccs.task_options.model_path">
            <value />
        </option>
        <option id="pbccs.task_options.min_predicted_accuracy">
            <value>0.9</value>
        </option>
        <option id="pbccs.task_options.max_drop_fraction">
            <value>0.34</value>
        </option>
        <option id="pbccs.task_options.min_zscore">
            <value>-3.4</value>
        </option>
        <option id="pbccs.task_options.polish">
            <value>True</value>
        </option>
        <option id="pbccs.task_options.by_strand">
            <value>False</value>
        </option>
        <option id="pbccs.task_options.model_spec">
            <value />
        </option>
        <option id="pbcoretools.task_options.score_mode">
            <value>asymmetric</value>
        </option>
        <option id="pbccs.task_options.report_file">
            <value>ccs_report.txt</value>
        </option>
        <option id="pbccs.task_options.min_length">
            <value>500</value>
        </option>
        <option id="pbccs.task_options.min_read_score">
            <value>0.65</value>
        </option>
        <option id="pbccs.task_options.min_snr">
            <value>3.75</value>
        </option>
        <option id="pbccs.task_options.max_length">
            <value>5000</value>
        </option>
        <option id="pbccs.task_options.min_passes">
            <value>3</value>
        </option>
    </task-options>
</pipeline-preset-template>

sub.sh

#!/bin/bash

PATH_TO_BIN=/media/ephemeral0/smrtbin
PATH_TO_SUBREADSET=/media/ephemeral0/smrt_wrapper/smrt/userdata/data_root/5_E01/m54048_170422_091135.subreadset.xml
PATH_TO_BARCODES=barcodes.fasta

$PATH_TO_BIN/pbsmrtpipe pipeline-id pbsmrtpipe.pipelines.sa3_ds_barcode_ccs -e eid_subread:$PATH_TO_SUBREADSET -e eid_barcode:$PATH_TO_BARCODES --preset-xml preset.xml