nextflow environment fix #4
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
typo
Previously, there were instructions to install nextflow. They are removed but nextflow was not added to environment file.
The docker container had caused issues for us due to sra-tools configuration. It was configured as far as i can tell in the image. I think the requirement was removed on V3.0.1. This image uses the latest version of sra-tools and has worked without issues so far. It's built from this: ```FROM ayyuan/fasterq-dump:1.0 # Download, extract sratoolkit, and clean up. RUN wget -q https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz -O /tmp/sratoolkit.tar.gz \ && tar -xzf /tmp/sratoolkit.tar.gz -C /opt \ && rm -r /tmp/sratoolkit.tar.gz /opt/sratoolkit.3.0.0-ubuntu64 # Set the PATH environment variable. ENV PATH="/opt/sratoolkit.3.1.1-ubuntu64/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" # Set the default command to run CMD ["bash"]```
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Adding nextflow to environment and fixing typo on readme - not tested.
updating the sra-tools container to avoid config bug - tested.