clcserver
, text information is returned providing a summary of the steps taken, and the locations, in ID form, of any files generated. The file containing this information will, by default, be created in the current directory and will be called result.txt
. You can use the -O
option for the clcserver
command if you wish to specify an alternative file to be written to.
An example of contents in a typical result file is shown below. In this case the file that was generated after running the trim algorithm using a sequence list called reads
as input. The result file lists the three files that were produced.
// Name: reads trimmed ClcUrl: clc://127.0.0.1:7777/-268177574-YCAAAAAAAAAAAAPc673b0db8c5e724f--5d66a991-12d75090d93--7fff // // Name: reads report ClcUrl: clc://127.0.0.1:7777/-268177574-ADAAAAAAAAAAAAPc673b0db8c5e724f--5d66a991-12d75090d93--7fff // // Name: Trim Sequences log ClcUrl: clc://127.0.0.1:7777/-268177574-CAAAAAAAAAAAAAPc673b0db8c5e724f--5d66a991-12d75090d93--7fff //
When creating pipelines stitching together several analyses, you parse the result file to get the location of the data produced, which is needed as input for the next algorithm.
The result file is just a text file, but it can still be a challenge to parse it to get the necessary CLC URLs. Thus, we provide a tool called clc_result_parser
to help with this. It searches the result file for a text expression you provide, and returns the CLC URL for files where a match to that text has been found in the Name:
field. The Name
field will contain the name of the input data along with a description of the type of data held in that file location.
In the case above, you would probably search for the trimmed reads to use for further analysis, which could be done with a command like this:
clcresultparser -f result.txt -c trimmedHere, the following text would be returned:
clc://127.0.0.1:7777/-268177574-YCAAAAAAAAAAAAPc673b0db8c5e724f--5d66a991-12d75090d93--7fff
The options for the clcresultparser
program are:
Name
field of the result file. If nothing is found, the exit code is 1.
Name
field of the result file.
false
as the argument to this option to stop log files from being returned. This is equivalent to excluding all names ending with log
, or log
with a number suffix. The latter are generated when there is more than one log file in the same folder.
clcresultparser
command as arguments to -i
options for the next analysis, simply provide "-i" as as the argument for the -p
flag.
echo $?
.