Dockerfile

[fgypas]

Hi

Is there a Dockerfile available for vast-tools? In this way, one could skip the installation process.

Thank you in advance Foivos

[evanfloden]

I did one a while ago for the dependencies here: https://github.com/evanfloden/vast-tools-nf/blob/master/Dockerfile

Looking back I didn't include vast-tools itself. Not sure why not but it would be easy enough to add a git clone.

[fgypas]

Thanks @evanfloden . At least it is a good starting point. So the repo I found at docker hub (https://hub.docker.com/r/skptic/vasttools/) is based on a different Dockerfile? vast-tools is available there.

[evanfloden]

It will be the same one I believe as I created that one.

But I should update the Dockerfile in my repo now anyway.

Gimmie 15 min.

[evanfloden]

Updated and included the vast-tools repo in the image.

Note that this does not take care of the VASTDB which should be downloaded and linked.

I will attempt to update the workflow which takes care of these details.

Image is on dockerhub evanfloden/vasttools:v2.0.2 and Dockerfile is here.

[fgypas]

I tried it and I think there is a problem with Bowtie. It's not in PATH. Does it work for you? When I run in the container the command:

bowtie-1.2.1.1/bowtie --help

I get the following error:

/usr/bin/env: python: No such file or directory

[fgypas]

I think that python is a dependency. I would change the bowtie part to the following:

RUN apt-get install -y python && \
wget -q https://github.com/BenLangmead/bowtie/releases/download/v1.2.1.1/bowtie-1.2.1.1-linux-x86_64.zip && \
unzip bowtie-1.2.1.1-linux-x86_64.zip && \
rm bowtie-1.2.1.1-linux-x86_64.zip && \
ln -s /bowtie-1.2.1.1/bowtie /usr/bin/bowtie

[evanfloden]

Thanks! I have added that line to the above Dockerfile and pushed the image to dockerhub.

Let me know if there are any other problems.

[fgypas]

Thanks a lot. I think it works just fine now.