itsers/neighbors repository overview

⁠Introduction

This container includes pre-compiled programs from the EvolBioInf github repository (https://github/evolbioinf⁠) for marker sequence search using whole genome sequences:

• Neighbors package (find taxonomic neighbors)
• phylonium (fast genetic distance calculation)
• fur package (find unique genomic regions)
• biobox package (manipulate sequences, trees, etc.)

Auxiliary tools on-board:

• datasets package (access NCBI databases from Unix CLI)
• blast+ (pairwise sequence alignment)
• gnuplot (draw plots, in particular, phylogenetic trees)

⁠Installation

To install the container:

docker pull itsers/neighbors

⁠Preparing host machine

Enable X11 connections to allow docker containers to display plots on the screen:

xhost +

This message should appear upon successful execution:

'access control disabled, clients can connect from any host'.

⁠Running the container

We recommend these options to run the container:

docker run -it --env="DISPLAY" --net=host -v
~/neighbors_share:/home/jdoe/neighbors_share -h neighbors
--detach-keys="ctrl-@" itsers/neighbors

When container is turned on successfully, you will see your username changed to jdoe, and the host name changed to neighbors in the current shell instance:

>jdoe@neighbors:~$

The initial user password for jdoe is: password.

To stop the container and return to the host shell, type exit or press Ctrl+D.

The flags usage explained:

• -it runs the container in CLI interactive mode

• --env="DISPLAY" and --net=host: these are needed to display graphic output from inside the container

• -v ~/neighbors_share:/home/jdoe/neighbors: this creates a folder shared between the neighbors container (/home/jdoe/neighbors_share) and your /home directory (/home/username/neighbors_share). With this, you can use the container to operate with your own data and save the results on your machine that hosts the container. Just make sure that you have saved your results at /home/jdoe/neighbors_share before stopping the container.

• --detach-keys="ctrl-@" is used here to override the default key sequence (Ctrl+P, Ctrl+Q) with Ctrl+Shift+2 for switching between interactive mode and daemon (background) mode. This frees the sequence Ctrl+P to be used alongside with Ctrl+N to navigate the shell command history within the container.

-h neighbors sets the host name inside the container.

⁠Documentation and tutorial

There is a file neighborsDoc.pdf at /home/jdoe describing the programs of the neqighbors package and providing a tutorial on neighbors-based analysis. You can move or copy the file to the /home/jdoe/neighbors_share folder and open it in your host operating system. If you want to open the PDF within the container, install a PDF viewer (for example, evince) inside the container:

apt-get install evince
evince neighborsDoc.pdf

Make sure that X11 connections are enabled beforehand (see above).

⁠Contacts

If you experience problems with the container, please open an issue at https://github.com/EvolBioInf/neighbors. To report bugs and errors from neighbors, fur, or biobox specifically, please open issues in the respective GitHub repos: https://github.com/EvolBioInf/neighbors, https://github.com/EvolBioInf/fur, or https://github.com/EvolBioInf/biobox.

⁠References

Haubold, B., Klötzl, F., Hellberg, L., Thompson, D., & Cavalar, M. (2021). Fur: Find unique genomic regions for diagnostic PCR. Bioinformatics, 37(15), 2081-2087. (https://doi.org/10.1093/bioinformatics/btab059⁠)

Klötzl, F., & Haubold, B. (2020). Phylonium: fast estimation of evolutionary distances from large samples of similar genomes. Bioinformatics, 36(7), 2040-2046. (https://doi.org/10.1093/bioinformatics/btz903⁠)

https://github.com/EvolBioInf/biobox⁠

Kans, J. (2022). Entrez direct: E-utilities on the UNIX command line. In Entrez Programming Utilities Help [Internet]. National Center for Biotechnology Information (US). (https://www.ncbi.nlm.nih.gov/books/NBK179288/⁠)

National Center for Biotechnology Information (US), & Camacho, C. (2008). BLAST (r) Command Line Applications User Manual (p. 30). National Center for Biotechnology Information (US). (https://www.ncbi.nlm.nih.gov/books/NBK279690/⁠)