fastp
fastp copied to clipboard
OpenGene
How to pull by version?
I built fastp in a docker image and it was working with v0.22.0 (it currently works on my local machine however I build that docker image over a week ago); however with issue #361 when I build a docker image in my CI/CD on AWS and then run a batch job I get the multithreading error.
In my dockerfile I have,
RUN wget http://opengene.org/fastp/fastp && \
chmod a+x ./fastp && \
cp fastp /bin/fastp
Is it possible to pin v0.22.0? when I download from http://opengene.org/fastp/fastp?
I restore the prebuilt fastp on opegene.org to v0.22.0.
In future I will provide a list to get historical builds.
I second the desire for version history, and keeping a few older releases available (at least the non-beta release) if possible. The release of v0.23.0 with the multithreading error broke our pipelines and it took some time to detect because it was a silent release. It would be better for software and pipeline version control if multiple releases are available (all downloading as fastp since that's the command name, instead of fastp.0.22.0 which requires extra steps to change). Thanks, and thank you for maintaining this tool. It's very useful.
EDIT: another option would be make fastp available with pip, which allows version control. (We don't use Anaconda/Miniconda because they make our containers too heavy.)
I prefer it the way it is b/c I setup my dockerfile as:
FROM ubuntu:20.04
ARG DEBIAN_FRONTEND=noninteractive
ARG VERSION=0.22.0
# Application installation
RUN wget -O fastp http://opengene.org/fastp/fastp.${VERSION} && \
chmod a+x ./fastp && \
cp fastp /bin/fastp
I do the same now (I just recently changed it). I didn't know before checking this thread that specific versions were available just by specifying a tag after fastp.
If they have always been available that way, then that's my bad. I just couldn't find an easy way to track releases and their changes online, which is helpful for troubleshooting and for dealing with version control in general.
On Fri, Sep 24, 2021 at 3:29 PM Daniel Donovan @.***> wrote:
I prefer it the way it is b/c I setup my dockerfile as:
FROM ubuntu:20.04
ARG DEBIAN_FRONTEND=noninteractive ARG VERSION=0.22.0
Application installation
RUN wget -O fastp http://opengene.org/fastp/fastp.${VERSION} &&
chmod a+x ./fastp &&
cp fastp /bin/fastp— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OpenGene/fastp/issues/362#issuecomment-926871155, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGBWOQROW6DYD6SWWVDJHCTUDTGTLANCNFSM5EQKDNCA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
-- Jessica Rowell
http://opengene.org/fastp/fastp has been restored to the version with latest code (may be not released).
From v0.20.0, all released versions will be kept on server. For example, if you want to use v0.22.0, please download: http://opengene.org/fastp/fastp.0.22.0
Awesome - this is very helpful. Thank you! I appreciate your help and efforts.
On Sat, Sep 25, 2021 at 12:00 AM Shifu Chen @.***> wrote:
http://opengene.org/fastp/fastp has been restored to the version with latest code (may be not released).
From v0.20.0, all released versions will be kept on server. For example, if you want to use v0.22.0, please download: http://opengene.org/fastp/fastp.0.22.0
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OpenGene/fastp/issues/362#issuecomment-927005912, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGBWOQREQ3N6FZSFOAKLUPDUDVCNBANCNFSM5EQKDNCA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
-- Jessica Rowell