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pfcarrier/docker_mermade

By pfcarrier

•Updated over 8 years ago

dockerized mermade application for analyzing DNA Bind-n-Seq

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pfcarrier/docker_mermade repository overview

⁠Intent

Sharing a way to get up and running quickly with mermade through containerization.

Mermade :

⁠Quick startup

Install docker, then run the following :

$ git clone https://github.com/pfcarrier/docker_mermade.git
$ cd docker_mermade
$ ./build
$ ./run # open a terminal in the container with your PWD mounted in /work
$ run_mermade.pl

The last command should output the syntax of the run_mermade.pl script

If you are using docker-for-windows try the following instead to download the already build image and run it:

$ docker run -v c:\full_path_to_your_fastq_file:/work -it pfcarrier/docker_mermade bash

In the command above "c:\full_path_to_your_fastq_file" is usually replaced with the directory on your laptop that contain your sequence ( E.g. xxxxx.fastq) file.

Note that the directory should also contain the barcode.txt and background.txt file.

When you are inside the container the /work/ directory you are starting in is a mount point to c:\full_path_to_your_fastq_file. This allow mermade to access any file that is there. When inside the container You can run the ls command to confirm that ; you should see the file it contain listed in the output.

⁠How to run mermade with your data

Place the following file in the directory that the container have access to, if you are using docker-for-windows this will be c:\full_path_to_your_fastq_file, if you are using linux this will be the location where you cloned this repos. This location is referd later in this document as the work directory.

  • background.txt
  • barcode.csv
  • sequencefile.fastq.gz

Run the following within the container work directory. E.g.

$ rm -rf mermade_output.db wdir
$ run_mermade.pl -o mermade_output.db -d wdir -b background.txt PRO1071_S1_libDNA_raw_NoIndex_L001_R1.fastq.gz barcode.csv

# Using test file provided by the `Korf Lab` ( see below for download link )
$ rm -rf mermade_output.db wdir
$ run_mermade.pl -o mermade_output.db -d wdir -b background.txt BnS13.fastq.gz BnS13-barcodes.csv

⁠How to generate a report

From within the container run

$ reporter.pl mermade_output.db 5 report_output_1 AAA AAC AAG AAT ACA
# ^^ if you run again change report_output_1 for report_output_2 and so on

You can view the generated reports by opening the following file with your browser. The file is located in the work directory.

  • report_output_1/index.html

⁠Test data to play with mermade

⁠Is there a docker hub automated build images ?

Yes

Tag summary

Content type

Image

Digest

Size

181.8 MB

Last updated

over 8 years ago

docker pull pfcarrier/docker_mermade