Molecular phylogenetics exercise with docker (working)

Molecular Phylogenetics Exercise From Data Set Creation to Hypothesis Testing Akifumi Tanabe 2015/10/20 https://www.fifthdimension.jp/documents/molphytextbook/molphytextbook.ja.html

Struggling to move with docker (working)

java

I want to choose the best Java Docker image https://k11i.biz/blog/2018/05/17/base-docker-images-for-java/

Think about recommended Docker images after Java 11 release https://k11i.biz/blog/2018/10/29/base-docker-images-for-java11/

Summary of Java support 2018 https://qiita.com/nowokay/items/edb5c5df4dbfc4a99ffb

A quick note on using jshell with the official Docker image of the JDK https://qiita.com/hi5san/items/d2f2fc77683530073267

$ docker run -v /tmp/work:/tmp/work -it openjdk /bin/bash
docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?.
See 'docker run --help'.

# apt update; apt -y upgrade
bash: apt: command not found

openjdk

https://hub.docker.com/_/openjdk

adoptopenjdk

https://hub.docker.com/_/adoptopenjdk

adoptopenjdk/openjdk11 - Docker Hub https://hub.docker.com/r/adoptopenjdk/openjdk11/

$ docker run -v /tmp/work:/tmp/work -it adoptopenjdk/openjdk11:alpine-slim  /bin/bash
Unable to find image 'adoptopenjdk/openjdk11:alpine-slim' locally
alpine-slim: Pulling from adoptopenjdk/openjdk11
c9b1b535fdd9: Pull complete 
c27d8e400471: Pull complete 
deee333e69e3: Pull complete 
951b04c9812e: Pull complete 
Digest: sha256:9f18e54372102ed0cd3cb782d49d147d03cc2f3a8f08f096ee95b84563685441
Status: Downloaded newer image for adoptopenjdk/openjdk11:alpine-slim
docker: Error response from daemon: OCI runtime create failed: container_linux.go:346: starting container process caused "exec: \"/bin/bash\": stat /bin/bash: no such file or directory": unknown.

Reference

Try various JDKs with Docker https://qiita.com/kikutaro/items/d140f519253f276b94e0

Problems encountered using the OpenJDK image maintained by the Docker community https://matsumana.info/blog/2018/10/13/openjdk11-docker/

Self reference

Biological statistics https://qiita.com/kaizen_nagoya/items/6ebfb7bae0495424061e