Getting Started - Oshlack/necklace GitHub Wiki

• bash command line
• Java 1.8 - You can also use earlier versions of Java, but need to perform de novo transcriptome assembly outside Necklace. See Options.
• wget - Only required for installing Necklace and not for running it. If the required tools are installed manually, this is not needed.
• g++

1. Download the latest release
2. Unzip and untar the package in an appropriate directory:

tar -zxvf <filename>

or

unzip <filename>

3. Change into the necklace subdirectory and run the install script for linux:

./install_linux64.sh

or for MacOS:

./install_mac.sh

This will install all required software, such as the HISTAT2 aligner, StringTie and Trinity assembler. 4. Check that all tools were installed correctly

cat tools.groovy

All paths in this file should be set. If a path is missing, you will need to manually install the software then provide the path to the command in tools.groovy.

If you wish to specify your own installation of a tool (for example if you are running on a cluster with modules installed), you can modify the paths in tools.groovy as needed. Note that the installation script will generate the file "tools.groovy" when it runs. However, please note that Necklace might not work with different version numbers of tools (for example earlier versions of Trinity don't include all the options that Necklace expects).

1. Set up a configuration file with paths to the input data. The paths may either be absolute or relative (to the directory where you will run necklace from). If the input gzipped fastq files have a different file naming convention than <sampleID>_<ReadEnd>.fastq.gz, see Options. Use the following as a template:

// sequencing data
reads_R1="<path>/<sample1_readEnd1>.fastq.gz,<path>/<sample2_readEnd1>.fastq.gz,...."
reads_R2="<path>/<sample1_readEnd2>.fastq.gz,<path>/<sample2_readEnd2>.fastq.gz,...."
//leave reads_R2="" for single end reads

//The reference genome and its annotation
annotation="<path>/<annotation_1>.gtf <path>/<annotation_2>.gtf ..."
genome="<path>/<genome>.fa"

//The protein sequences from related species
proteins_related_species="<path>/<related_species_protein_sequences>.fa"

//Other Necklace options such as pre-assemblies and tools specific options can
//be specified in this file or on the command line

2. Necklace is a bpipe pipeline and therefore runs through bpipe. It can be run with the following command:

<path_to_necklace>/tools/bin/bpipe run <path_to_necklace>/necklace.groovy <configuration file>

See our demo for a small dataset with which to test the installation and see what the output looks like.