- install nextflow
curl -s https://get.nextflow.io | bash
- pull the singularity image from the singularity hub
singularity pull shub://maxemil/Biodiversity-pipeline:master
- execute the pipeline with input.fasta, references.fasta (e.g. ) and information on the ecology of sequences
nextflow run maxemil/Biodiversity-pipeline --input_fasta input.fasta \
--reference_sequences references.fasta \
--environment_information ecology.tab \
--output_directory output \
-with-singularity maxemil-Biodiversity-pipeline-master.img
- java >= 7
- nextflow (http://nextflow.io)
- singularity (recommended, http://singularity.lbl.gov/)
- MALT (http://ab.inf.uni-tuebingen.de/software/malt/)
- MEGAN6 (http://ab.inf.uni-tuebingen.de/software/megan6/)
- FUNGuild (https://github.com/UMNFuN/FUNGuild)
- vsearch (https://github.com/torognes/vsearch)
- spaced words (http://spaced.gobics.de/)
- python3
- pandas
- numpy
- requests
- R
- vegan
- picante
- VennDiagram
- To run an example analysis and check if the results are as expected, run
nextflow run maxemil/Biodiversity-pipeline --input_fasta test/input.fasta \
--reference_sequences test/references.fasta \
--environment_information test/ecology.tab \
--output_directory test/output \
-with-singularity maxemil-Biodiversity-pipeline-master.img