Before you use the pipeline you always need to ensure that the miniconda environment is in your environment's path. You will want to look at the install for more details
You can run a single sample by using the runsample.py command. There are 2 examples that you can use. Sample 780 and Sample 947 which are both located in the ngs_mapper/tests/fixtures/functional directory. Inside that directory you will see directory for each sample which contains its reads as well as the reference for each of them and a config file for each sample. You can ignore the config file as it is used by the tests to determine if the sample ran correctly or not
You can use runsample.py on them as follows:
mkdir -p tdir && cd tdir
runsample -od 780 ../ngs_mapper/tests/fixtures/functional/780{,.ref.fasta} 780
runsample -od 947 ../ngs_mapper/tests/fixtures/functional/947{,.ref.fasta} 947This will create a temporary directory called tdir and cd into it then run both sample 780 as well as 947 and put their results inside of their own directory named after themselves.
From there you can explore them on your own
<<<<<<< HEAD The following requires that you have docker installed on your computer. You can get docker from visiting https://www.docker.com/ and clicking on the Operating System from the 'Get Docker' dropdown.
The following is simply an example of how to run the test data set that resides in the ngs_mapper git repository. This is to simply get you familiar with how to run the pipeline using docker.
To run the following example you will need to clone the ngs_mapper git repository to your local computer
git clone https://github.com/VDBWRAIR/ngs_mapper.gitOnce you have cloned the repo you can then run through the following.
In the below command we are instructing docker to mount the ngs_mapper/tests/fixtures/functional directory from your local computer to /NGSDATA inside of the docker container when it runs.
In the below command we are instructing docker to mount the ngs_mapper/tests/fixtures/functional directory from your local computer to /data inside of the docker container when it runs.
It is also mounting the current directory you are running the command from as /output inside the container.
You can then see that it is running the runsample command the same as you would normally run it and pointing to the /data/947 directory to read samples data from(as well as the reference file) and then sending all the output to the /output/947 directory.
After the pipeline is finished running you would find the 947 directory under the output directory in your local computer.
The vdbwrair/ngs_mapper:latest instructs docker to use the latest version of ngs_mapper from dockerhub.
If you want to use a different version you can replace latest with any tag listed under https://hub.docker.com/r/vdbwrair/ngs_mapper/tags/
For example: vdbwrair/ngs_mapper:v1.5.4 would use the v1.5.4 version of ngs_mapper.
mkdir -p output
docker run -it -v $PWD/output:/output -v $PWD/ngs_mapper/tests/fixtures/functional:/NGSDATA vdbwrair/ngs_mapper:latest runsample /NGSDATA/947 /NGSDATA/947.ref.fasta -od /output/947 947Once you have completed this you should have a better understanding of how to use docker to run ngs_mapper. To run your own data you can replace $PWD/ngs_mapper/tests/fixtures/functional
with the path to your data and then change the /NGSDATA/947 to reference where your samples would reside.
For example, if your samples were in /some/path/sampledata/sample1, then you would use something like the following:
mkdir -p output
docker run -it -v $PWD/output:/output -v /some/path/sampledata:/NGSDATA vdbwrair/ngs_mapper:latest runsample /NGSDATA/sample1 /NGSDATA/ref.fasta -od /output/947 947If your reference file exists somewhere outside of /some/path/sampledata you can use another -v option for docker to make it available within the docker container when it runs
docker run -it -v /path/to/references:/references -v $PWD/output:/output -v /some/path/sampledata:/NGSDATA vdbwrair/ngs_mapper:latest runsample /NGSDATA/sample1 /references/ref.fasta -od /output/947 947