Since I first knew of Docker, I thought it might be the solution for several problems we are usually facing at the lab. I work as a Data Analyst for a small Biology research group. I am using Snakemake for defining the -usually big and quite complex- workflows for our analyses. From Snakemake, I usually […]
what is the “best practice” workflow of testing dockerized applications in a CI/CD process? Run tests and then create the container Create the container and run test against interface of containerized app something else?
I’m trying to get a bunch of very big files into a docker container while using CWL. When using the default method of file-inputs via job.yml: input_file: class: File path: /home/ubuntu/data/bigfile.zip the CWL runner somehow copies the file and gets stuck. Is there an easy way of just mounting a directory directly into a docker […]
Everytime I change a file in the nodejs app I have to rebuild the docker image. This feels redundant and slows my workflow. Is there a proper way to sync the nodejs app files without rebuilding the whole image again, or is this a normal usage?
I’m trying to imagine a workflow that could be applied on a scientific work environment. My work involves doing some scientific coding, basically with Python, pandas, numpy and friends. Sometimes I have to use some modules that are not common standards in the scientific community and sometimes I have to integrate some compiled code in […]
I already have set up a github repository with 3 branches (master, dev and docker). I already set up successfully and linked the automated build on dockerhub. Each time a push is done on Github an image is built on Dockerhub with different tag (latest for master, beta for dev and alpha for docker). This […]
I’m just getting started with Docker. With the official NGINX image on my OSX development machine (with Docker Machine as the Docker host) I ran up against the bug with sendfile and VirtualBox which means the server fails to show changes I make to files. The workaround for this is to use a modified nginx.conf […]
I am trying to understand how development is done efficiently with dockerized applications, specifically on Kubernetes. I am struggling to find the proper way to go about live editing containers. In the past with Docker, I would just use something like Nodemon to watch for files to change locally and then when I had the […]
As a Vagrant user, when trying Docker I noticed one significant difference between development workflow with Vagrant and with Docker – with Docker I need to rebuild my image every time from scratch, even if I made minor changes in code. This is major problem for me, because the process of image rebuilding oftenly very […]
What’s the proper development workflow for code that runs in a Docker container? Solomon Hykes said that the “official” workflow involves building and running a new Docker image for each Git commit. That makes sense, but what if I want to test a change before committing it to the Git repo? I can think of […]