This repository contains the docker images used by the ACTG course Thes are already available for use via Docker or Singularity here: https://hub.docker.com/orgs/systemsgenetics/repositories
The following is a list of tool names currently supported by this Makefile
| Tool | Version |
|---|---|
| bedtools | 2.30.0 |
| biopython | 1.81 |
| blast | 2.14.0 |
| braker | 2.1.6 |
| busco | 5.4.3-0 |
| bwa | 0.7.17 |
| bwa | 0.7.18 |
| edta | 2.0.1 |
| edta | 2.2.2 |
| emboss | 6.6.0 |
| fastp | 0.23.2 |
| fastp | 0.24 |
| fastqc | 0.11.9 |
| fastqc | 0.12.1 |
| genespace | 1.2.3 |
| hic_qc | 6881c33 |
| hifiasm | 0.16.1 |
| hifiasm | 0.24.0 |
| jellyfish | 2.2.10 |
| jellyfish | 2.3.1 |
| juicer | 1.22.01 |
| kraken | 2.1.3 |
| mcscanx | b1ca533 |
| meryl | 1.4.1 |
| mitohifi | 2.2 |
| multiqc | 1.13a |
| multiqc | 1.26 |
| mummer | 3.23 |
| mummer | 4.0.0rc1 |
| novoplasty | 4.3.1 |
| novoplasty | 4.3.5 |
| orthofinder | 2.5.5 |
| pasa | 2.5.2 |
| r-base | 4.1.3 |
| r-base | 4.4.2 |
| repeatmasker | 4.1.2.p1 |
| samtools | 1.15.1 |
| samtools | 1.21 |
| sra-tools | 2.11.0 |
| star | 2.7.10a |
| trinity | 2.13.2 |
| yahs | 1.2.2 |
| yahs | 1.2a.2-0 |
To build all docker images:
makeTo test that all images are working run the following run the following:
make testThe version of the software should be printed to the screen. This test only ensures the software can be run, no that it is working as expected.
To push all docker images to DockerHub
make pushYou can build, test, push and run a single tool by changing to the tool directory, then to the toll version firset and then running the following commands.
To build the tool
makeTo test the tool
make testTo push the tool to DockerHub
make pushTo run in interactive mode
make run