pegi3s/htseq

Sponsored OSS

By i3S

Updated 2 months ago

HTSeq (https://htseq.readthedocs.io/en/latest/) Docker image.

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This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

This image facilitates the usage of HTSeq, a Python package for analysis of high-throughput sequencing data.

Using the HTSeq image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/htseq <script-name> [script arguments]

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the FASTA file you want to align.
  • <script-name> to the actual name of the script to be executed (e.g. htseq-qa or htseq-count.
  • [script arguments] with the argumetns required by the script.

Using the HTSeq image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/htseq <script-name> [script arguments]

Docker Pull Command

docker pull pegi3s/htseq