Install¶
Requirements¶
Hardware¶
- CPU
- Quad Core 2.5GHz or better
- More cores = faster run time when running multiple samples
- Faster GHz = faster each sample runs
- RAM
This really depends on your data size
If you are analyzing a 96 sample run then you should be fine with 1GB per CPU core
If you are analyzing a 24 sample run then you will probably need about 4GB per CPU core since there will be more data
Roche Utilities¶
If you intend on using the roche_sync
you will
need to ensure that the sfffile
command is in your PATH. That is, if you
execute $> sfffile
it returns the help message for the command.
This command should automatically be installed and put in your path if you install the Data Analysis CD #3 that was given to you with your Roche instrument.
MidParse.conf¶
If you inted on using the roche_sync
you may need
to edit the included ngs_mapper/MidParse.conf file before installing. This file is
formatted to be used by the Roche utilities and more information about how it is
used can be found in the Roche documentation.
Installation¶
Clone/Download the version you want
Clone the code
git clone https://github.com/VDBWRAIR/ngs_mapper.git cd ngs_mapper
Check which versions are available
git tag
Checkout the version you want(current version 1.4.2)
git checkout -b vX.Y.Z vX.Y.Z
Configure the defaults
You need to configure the ngs_mapper/config.yaml file.
Copy the default config to config.yaml
cp ngs_mapper/config.yaml.default ngs_mapper/config.yaml
Then edit the ngs_mapper/config.yaml file which is in yaml format
The most important thing is that you edit the NGSDATA value so that it contains the path to your NGSDATA directory.
The path you use for NGSDATA must already exist
mkdir -p /path/to/NGSDATA
Install
The project now comes with a much more simplified installer which is based on miniconda.
The following will install the project into the current directory that you are in.
./install.sh miniconda
PATH Setup
Once the project is installed you will need to setup your PATH environmental variable to include the
export PATH=$PWD/miniconda/bin:$PATH
You can put this into your .bashrc file inside your home directory so that any time you open a new terminal it automatically is run.
If you don’t setup your .bashrc you will have to run the export command from above every time you open a new terminal.
Verify install¶
You can pseudo test the installation of the pipeline by running the functional tests
ngs_mapper/tests/slow_tests.sh