Mkfifo and dx cat

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This applet performs a SAMtools count on an input file while minimizing disk usage. For additional details on using FIFO (named pipes) special files, run the command man fifo in your shell.

Named pipes require BOTH a stdin and stdout. The following examples run incomplete named pipes in background processes so the foreground script does not block.

To approach this use case, outline the steps for the applet:

1. Stream the BAM file from the platform to a worker.

2. While the BAM streams, count the number of reads present.

3. Write the result to a file.

4. Stream the result file to the platform.

Stream BAM file from the platform to a worker

First, establish a named pipe on the worker. Then, stream to the stdin of the named pipe and download the file as a stream from the platform using dx cat.

mkdir workspace
mappings_fifo_path="workspace/${mappings_bam_name}"
mkfifo "${mappings_fifo_path}" # FIFO file is created
dx cat "${mappings_bam}" > "${mappings_fifo_path}" &
input_pid="$!"

FIFO	stdin	stdout
BAM file	YES	NO

Output BAM file read count

Having created the FIFO special file representing the streamed BAM, you can call the samtools command. The samtools command reading the BAM provides the BAM FIFO file with a stdout. However, remember that you want to stream the output back to the Platform. You must create a named pipe representing the output file too.

mkdir -p ./out/counts_txt/

counts_fifo_path="./out/counts_txt/${mappings_bam_prefix}_counts.txt"

mkfifo "${counts_fifo_path}" # FIFO file is created, readcount.txt
samtools view -c "${mappings_fifo_path}" > "${counts_fifo_path}" &
process_pid="$!"

FIFO	stdin	stdout
BAM file	YES	YES
output file	YES	NO

The directory structure created here (~/out/counts_txt) is required to use the dx-upload-all-outputs command in the next step. All files found in the path ~/out/<output name> are uploaded to the corresponding <output name> specified in the dxapp.json.

Stream the result file to the platform

A stream from the platform has been established, piped into a samtools command, and the results are output to another named pipe. However, the background process remains blocked without a stdout for the output file. Creating an upload stream to the platform resolves this.

Upload as a stream to the platform using the commands dx-upload-all-outputs or dx upload -. Specify --buffer-size when needed.

dx-upload-all-outputs &
upload_pid="$!"

FIFO	stdin	stdout
BAM file	YES	YES
output file	YES	YES

Alternatively, dx upload - can upload directly from stdin, removing the need for the directory structure required for dx-upload-all-outputs.

dx upload - --path "${mappings_bam_prefix}_counts.txt" < "${counts_fifo_path}" &
upload_pid="$!"

When uploading a file that exists on disk, dx upload knows the file size and automatically handles any cloud service provider upload chunk requirements. When uploading as a stream, the file size is not known automatically and dx upload uses default parameters. These defaults are fine for most use cases, but you may need to specify an upload part size with the --buffer-size option.

Wait for background processes

With background processes running, wait in the foreground for those processes to finish.

wait -n  # "$input_pid"
wait -n  # "$process_pid"
wait -n  # "$upload_pid"

Without waiting, the app script running in the foreground finishes and terminates the job prematurely.

How is the SAMtools dependency provided?

The SAMtools compiled binary is placed directly in the <applet dir>/resources directory. Any files found in the resources/ directory are uploaded so that they are present in the worker's root directory. In this case:

├── Applet dir
│   ├── src
│   ├── dxapp.json
│   ├── resources
│       ├── usr
│           ├── bin
│               ├── < samtools binary >

When this applet is run on a worker, the resources/ folder is placed in the worker's root directory /:

/
├── usr
│   ├── bin
│       ├── < samtools binary >
├── home
│   ├── dnanexus

/usr/bin is part of the $PATH variable, so the samtools command can be referenced directly in the script as samtools view -c ....