Running apps on the Commandline¶
Navigate to the folder where your cloudgene.yaml file is located and start your workflow with the following command:
cloudgene run cloudgene.yaml <workflow parameters>
or if you installed an application you can start it by entering the name. For example:
cloudgene run hello-cloudgene
Running a pipeline with Hadoop steps¶
Cloudgene needs a Hadoop cluster to execute MapReduce steps. If Cloudgene is installed on the Hadoop Namenode you have to use the --conf
flag and provide the $HADOOP_CONF
folder. For example:
./cloudgene run cloudgene.yaml <workflow parameters> --conf /etc/hadoop/conf
Running Hadoop steps on a remote Hadoop cluster¶
Navigate to the folder where your cloudgene.yaml file is located and execute your workflow with the --host
flag to set the ip address of your remote Hadoop cluster:
./cloudgene run cloudgene.yaml <workflow parameters> --host <remote-ip>
Cloudgene executes your MapReduce steps on the remote cluster. You can use the --user
flag to set the username which should be used to execute your job (e.g. it uses the HDFS directory of this user for all files):
./cloudgene run cloudgene.yaml <workflow parameters> --host <remote-ip> --user <remote-user>