Tool:Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/)

Question

[pegi3sdocker]

Dear colleagues,

This is to let you know about our Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/, https://hub.docker.com/u/pegi3s/ ). As similar projects, our aim is to provide ready-to-use Docker images for bioinformatics software commonly used in genomics, transcriptomics, sequence analysis, and philogenetics (e.g. BLAST, FastQC, Clustal Omega, etc.).

We also focus in giving clear instructions on how to use the images and providing appropriate sample cases to test them easily (e.g. https://hub.docker.com/r/pegi3s/alter ). We have also created images for GUI-based software such as ADOPS (https://hub.docker.com/r/pegi3s/adops-gui ), TreeView X (https://hub.docker.com/r/pegi3s/treeviewx ) or SEDA (https://hub.docker.com/r/pegi3s/seda/ ), among others.

If you are interested in our project or would like to contribute with suggestions, you may contact us through [e-mail] or by creating an issue at the GitHub repository of the projet (https://github.com/pegi3s/dockerfiles/issues ).

Regards, the pegi3sdocker team.

[Devon Ryan]

Is there a reason that the Biocontainers project isn't sufficing for your needs?

[pegi3sdocker]

The main difference between our project and BioContainers is the fact that we provide detailed and clear information on how to run the Docker images, allowing researchers without a background in informatics to easily use such images. We also provide test cases when appropriate. Users may find also links to the developer's manuals of the scientific software. For those users wishing to use software with a graphical interface in Windows hosts, we provide a VirtualBox image with Docker installed.

Answer 1

[Hugo]

Dear colleagues,

Since the creation of the project, it has been growing constantly and we have recently created a new website: http://bdip.i3s.up.pt/

It is much more useful and comprehensive, including tutorials and quick-start guides, a powerfull image search (http://bdip.i3s.up.pt/search?showAll=true) and an improved image view (e.g. http://bdip.i3s.up.pt/container/blast).

We have also released docknrun, a Docker image that offers a graphical interface (GUI) that facilitates selecting, configuring and running images from our project: http://bdip.i3s.up.pt/getting-started#run-commands-gui

Regards,

The pegi3s Bioinformatis Docker Images Team.

[Jeremy Leipzig]

anyone who is using Chrome will see "bdip.i3s.up.pt doesn’t support a secure connection" and will assume this is some sketchy scam

you should get a self-signed certificate

openssl genrsa -out server.key 2048
openssl req -new -key server.key -out server.csr
openssl x509 -req -in server.csr -signkey server.key -out server.crt -days 365

put the cert in /etc/nginx/ssl/ and the key in /etc/nginx/ssl/private/

[barslmn]

sketchy scam

Http doesn't mean it would be a scam, but does show author of the website doesn't put much thought on the security.

Self-signed certificates will still show a warning on the first time. Let's encrypt offers free certificates and tools to install and auto-renew them. Also, newer web servers like traefik and caddy can handle the certificates automatically.