All Seal programs generally have the following invocation pattern:
./program [options] <input> <output>
Most programs can accept more than one input path (Seqal being the only exception). Also, while some Seal tools have their own specific options, there are a number of Seal options that all programs accept.
The input and output paths must be on an HDFS volume. If you like, you can use paths relative to the current user’s HDFS home directory, i.e., /user/<USERNAME>.
|Meaning||Short Opt||Long Opt|
|Number of reduce tasks to use.||-r <INT>||–num-reducers <INT>|
|Override default Seal config file ($HOME/.sealrc)||-sc <FILE>||–seal-config <FILE>|
|Set the value of a property||-D <prop=value>|
In addition, you can use most Hadoop options directly with the Seal tools. This is handy to override the cluster’s default settings.
./bin/prq -D bl.prq.min-bases-per-read=54 input output
./bin/seqal -D seal.seqal.remove_unmapped=true --trimq 15 input_1 input_2 output
./bin/read_sort --num-reducers 96 -D mapred.compress.map.output=true -ann ref.ann input output
If you find you’re setting the same property all the time, you should consider creating a Seal configuration file and saving your settings in it. The Seal tools will automatically load the file on start up. See the section Seal Config File for details.