CAMI Client

Introduction

The CAMI Client enables the following functionality:

The CAMI Client is a Java application, which requires Java 8 to be installed on the client machine. It can be downloaded from https://data.cami-challenge.org/camiClient.jar.

Downloading data files

Introduction

The CAMI client works by using reading the contents of a small linkfile - which is first downloaded locally from https://data.cami-challenge.org - and then using this to download the actual data files themselves.

The linkfile contains time-encoded links specific to each download and can be found under the desired download.

Instructions

From https://data.cami-challenge.org/camiClient.jar download the CAMI client jar


From https://data.cami-challenge.org log on, and download the linkfile for the dataset which you would like to download



Run the CAMI client, giving the -d argument and referencing the locally-downloaded linkfile and a target location for the data files (this location will be created if necessary). Note that if the linkfile has a space in the name, it will need to be wrapped in quotes.

java -jar camiClient.jar -d linkfileLocation targetLocation

eg.

java -jar camiClient.jar -d "/home/gary/Downloads/linkfile (29)" out


Wildcards

If only a subset of a download is required (for example only long reads, in a download containing both long and short reads), a pattern can be passed to the client using the -p option:

java -jar camiClient.jar -d linkfileLocation targetLocation -p pattern

eg.

java -jar camiClient.jar -d "/home/gary/Downloads/linkfile (29)" out -p long

The pattern can be any string which matches part of the name of a file to be downloaded. Another example might be, if a file strmgCAMI2_long_read_sample_65_reads.fq.gz has failed to download, and only this file is required, it could be selected using '-p long_read_sample_65_reads'


Threads

By default the client uses 10 threads for downloading. That is, it attempts to download ten download files in parallel. This can be adjusted using the -t parameter

java -jar camiClient.jar -d linkfileLocation targetLocation -t threads

eg.

java -jar camiClient.jar -d "/home/gary/Downloads/linkfile (29)" out -t 50