A container for using the R package SynExtend on the open science grid. The current SynExtend version is 1.14.0, and the several additional bioinformatics tools are included as well. With this current update, the container versioning has been edited to match the Bioconductor version.
This container is built to be a toolbox for working with genomic data in R on the Open Science Grid. It's current major package list includes:
- DECIPHER
- SynExtend
- dendextend
- ape
- igraph
- Samtools
- SRAToolkit
- SPAdes
- Unicycler
- Megahit
- SKESA
- bowtie2
- TreeDist
- deSolve
- Flye
- Canu
- Mash
- CWL
It contains several additional R packages as well as many required dependencies. BLAST, HMMER, and MCL are included as well, and their executables have been added to the default PATH. This container also has the NCBI EDirect tools, though users will need to supply their own API key. The read simulator tools pbsim and ART have also been recently added. This container is currently built from r-base:4.3.1.
Versions:
- BLAST
2.14.0 - HMMER
3.3.2 - MCL
22-282 - Bioconductor
3.18 - SRAToolkit
3.0.5
Details on SynExtend can be found here, and details on DECIPHER can be found here.
This container can be tested and used locally with docker pull npcooley/synextend:1.18.0 and docker run -i -t --rm npcooley/synextend sh. The container hypothetically supports plotting to the local display from R, but this functionality has only been tested on macOS, the localhost must be enabled with xhost. This can be done with xhost +${HOSTNAME}, and the display specified in the call to docker with docker run -it --rm -e DISPLAY=${HOSTNAME}:0 npcooley/synextend:1.18.0 sh. If these instructions work, in R capabilities()["X11"] should return TRUE. This feature currently isn't the most stable, but does allow for interactive plotting.
This container can be used as a singularity container on the Open Science Grid by specifying:
+SingularityImage = "/cvmfs/singularity.opensciencegrid.org/npcooley/synextend:1.18.0"
in your submit file.
If an installed tool is not working as expected, explicitly add the executable to the path with export:
export PATH=$PATH:/path/to/your/executable
in your wrapper script.
Nicholas Cooley npc19@pitt.edu