HML Blast Validation

Getting started

Installation

Git

Install nextflow by running the following command.

apt-get install git

For further documentation on git click here.

Nextflow

Install nextflow by running the following command.

curl -fsSL get.nextflow.io | bash

For further documentation on nextflow click here.

Docker

Click here for instructions on how to install docker. After you have docker installed run the following commands to start the docker daemon on your machine.

docker-machine start default
eval $(docker-machine env default)

Note

If you’re using a VPN the docker-machine will not work.

Overview

Parameters

--hml	HML file Required parameter
--output	Output directory Required parameter
--imgtdir	Location of where the BLAST IMGT database is located Default location is /opt/html on the docker container
--imgt	IMGT database version Default is 3200
--report	Binary flag for generating HTML validation report default is 1

Executing

./nextflow run nmdp-bioinformatics/flow-blast-hml -with-docker \
        nmdpbioinformatics/docker-blast-hml \
        --hml test_file.hml --outdir /path/to/output/dir

After running this command you should find a report and a validated file in the ouput directory you specified.

Running the Tutorial

Clone github repository

git clone https://github.com/nmdp-bioinformatics/flow-blast-hml
cd flow-blast-hml

Install nextflow

curl -fsSL get.nextflow.io | bash

Start docker machine

docker-machine start default
eval $(docker-machine env default)

Execute

./nextflow run nmdp-bioinformatics/flow-blast-hml -with-docker \
nmdpbioinformatics/docker-blast-hml \
--hml tutorial/ex00_ngsp_expected.xml \
--outdir tutorial/output --report 0

Developers

Contributing

1. Log into Github web interface with your username-nmdp account
2. Browse to the repo at https://github.com/nmdp-bioinformatics/flow-blast-hml, hit the Fork button.
3. Copy the clone URL from the Github web page for the fork (something like https://github.com/username-nmdp/pipeline.git)

4) Clone the fork .. code-block:: shell

git clone https://github.com/username-nmdp/flow-blast-hml.git cd flow-blast-hml

5) Add upstream as remote .. code-block:: shell

git remote add upstream https://github.com/nmdp-bioinformatics/flow-blast-hml

6) Pull and merge latest changes from upstream master to your local master branch .. code-block:: shell

git checkout master git pull upstream master git push

7) Create a new local feature branch .. code-block:: shell

git checkout -b new-feature-branch

8. Edit files locally

9) Commit changes to local feature branch .. code-block:: shell

git commit -m “made changes”

10) Push changes from local feature branch to remote feature branch on your fork .. code-block:: shell

git push origin new-feature-branch

11. Browse to the Github web page for your fork repo (something like https://github.com/username-nmdp/flow-blast-hml) and hit the new pull request button.
12. Edit the pull request description and hit create new pull request button.
13. Other contributors will review the changes in the pull request.
14. When the pull request looks good, it will be merged into the master branch.
15. Hit the delete branch button to delete your remote feature branch (the commits have been merge upstream, so it is no longer necessary).

16) Delete your local feature branch .. code-block:: shell

git branch -d new-feature-branch