CASAVA Quick Reference | Bcl Conversion and Demultiplexing | Running Bcl Conversion and Demultiplexing | Makefile Options for Bcl Conversion and Demultiplexing

Makefile Options for Bcl Conversion and Demultiplexing

The options for make usage in demultiplexing/analysis are described below.

Parameter

Description

nohup

Use the Unix nohup command to redirect the standard output and keep the “make” process running even if your terminal is interrupted or if you log out. The standard output will be saved in a nohup.out file and stored in the location where you are executing the makefile.

nohup make -j n &

The optional “&” tells the system to run the analysis in the background, leaving you free to enter more commands.

We suggest always running nohup to help troubleshooting if issues arise.

-j N

The -j option specifies the extent of parallelization, with the options depending on the setup of your computer or computing cluster.

r1

Runs Bcl conversion for read 1. Can be started once the last read has started sequencing.

POST_RUN_COMMAND_R1

A Makefile variable that can be specified either on the make command line or as an environment variable to specify the post-run commands after completion of read one, if needed. Typical use would be triggering the alignment of read 1.

POST_RUN_COMMAND

A Makefile variable that can be specified on the make command line to specify the post-run commands after completion of the run.

KEEP_INTERMEDIARY

The option KEEP_INTERMEDIARY tells CASAVA not to delete the intermediary files in the Temp dir after Bcl conversion is complete. Usage: KEEP_INTERMEDIARY:=yes

Parameter	Description
nohup	Use the Unix nohup command to redirect the standard output and keep the “make” process running even if your terminal is interrupted or if you log out. The standard output will be saved in a nohup.out file and stored in the location where you are executing the makefile. nohup make -j n & The optional “&” tells the system to run the analysis in the background, leaving you free to enter more commands. We suggest always running nohup to help troubleshooting if issues arise.
-j N	The -j option specifies the extent of parallelization, with the options depending on the setup of your computer or computing cluster.
r1	Runs Bcl conversion for read 1. Can be started once the last read has started sequencing.
POST_RUN_COMMAND_R1	A Makefile variable that can be specified either on the make command line or as an environment variable to specify the post-run commands after completion of read one, if needed. Typical use would be triggering the alignment of read 1.
POST_RUN_COMMAND	A Makefile variable that can be specified on the make command line to specify the post-run commands after completion of the run.
KEEP_INTERMEDIARY	The option KEEP_INTERMEDIARY tells CASAVA not to delete the intermediary files in the Temp dir after Bcl conversion is complete. Usage: KEEP_INTERMEDIARY:=yes

Note

If you specify one of the more specific workflows and then run a more general one, only the difference will get processed. For instance:

make -j N r1

followed by:

make -j N

will do read 1 in the first step, and read 2 the second one.

CASAVA v1.8.2 Quick Reference Help