How to use the containers#
First pull a Docker or Singularity container, see installation. For this tutorial, we use a general mechanism for persisting data, which allows to create and modify files on the host system from within the container. We use the c-elegans-chrI-example with the c-elegans-test.yaml configuration file, see also How to run the pipeline.
Note
You can also launch a container with an interactive shell e.g. docker run -it quay.io/biocontainers/rpbp:3.0.1--py310h30d9df9_0 /bin/bash or singularity shell rpbp.sif. With singularity shell, $HOME is mounted by default.
Attention
In the following, do not forget to modify the tag 3.0.1--py310h30d9df9_0 according to what you pulled! For Singularity, adjust the name of the Singularity image format file rpbp.sif and/or the path according to your needs.
How to run the pipeline#
To run the pipeline, change the paths in the configuration file to point to the location where the directory is mounted in the container. You can do this using a text editor, or simply by modifying the file in place
sed -i 's|/path/to/your/c-elegans-example|/data|g' c-elegans-test.yaml
Important
Default parameters were modified for the example and included in the configuration file. If you use this configuration file as a general template for your data, do not forget to remove everything below the line “REMOVE BELOW THIS LINE IF YOU USE THIS CONFIGURATION FILE AS TEMPLATE FOR YOUR DATA”.
You can now create the genome indices and annotations. For this small example, it is important to downscale the STAR --genomeSAindexNbases parameter as follows
docker run --volume `pwd`:/data quay.io/biocontainers/rpbp:3.0.1--py310h30d9df9_0 prepare-rpbp-genome /data/c-elegans-test.yaml --star-options "--genomeSAindexNbases 10" --num-cpus 4 --logging-level INFO --log-file /data/rpbp-genome.log
singularity run --bind `pwd`:/data rpbp.sif prepare-rpbp-genome /data/c-elegans-test.yaml --star-options "--genomeSAindexNbases 10" --num-cpus 4 --logging-level INFO --log-file /data/rpbp-genome.log
The file rpbp-genome.log contains logging output for the reference preprocessing. You now have a new directory called WBcel235.79.chrI with genome indices and annotations.
Finally, run the ORF discovery pipeline
docker run --volume `pwd`:/data quay.io/biocontainers/rpbp:3.0.1--py310h30d9df9_0 run-all-rpbp-instances /data/c-elegans-test.yaml --merge-replicates --run-replicates --keep-intermediate-files --num-cpus 4 --logging-level INFO --log-file /data/rpbp-pipeline.log
singularity run --bind `pwd`:/data rpbp.sif run-all-rpbp-instances /data/c-elegans-test.yaml --merge-replicates --run-replicates --keep-intermediate-files --num-cpus 4 --logging-level INFO --log-file /data/rpbp-pipeline.log
The file rpbp-pipeline.log contains logging output for the different processing steps. You now have four new directories (with-, without-) including output from Flexbar, Bowtie2, and STAR, and directories with Rp-Bp output: metagene-profiles, orf-profiles, and orf-predictions. The orf-predictions include the output for each sample c-elegans-rep-1 and c-elegans-rep-2 as well as for the merged replicates c-elegans-test.
How to summarize the results and launch the apps#
Prepare the summary output for the profile construction dashboard
docker run --volume `pwd`:/data quay.io/biocontainers/rpbp:3.0.1--py310h30d9df9_0 summarize-rpbp-profile-construction /data/c-elegans-test.yaml --num-cpus 4 --logging-level INFO --log-file /data/rpbp-profile-summary.log
singularity run --bind `pwd`:/data rpbp.sif summarize-rpbp-profile-construction /data/c-elegans-test.yaml --num-cpus 4 --logging-level INFO --log-file /data/rpbp-profile-summary.log
and for the predictions dashboard
docker run --volume `pwd`:/data quay.io/biocontainers/rpbp:3.0.1--py310h30d9df9_0 summarize-rpbp-predictions /data/c-elegans-test.yaml --no-replicates --circos-bin-width 10000 --circos-show-chroms I --logging-level INFO --log-file /data/rpbp-predictions-summary.log
singularity run --bind `pwd`:/data rpbp.sif summarize-rpbp-predictions /data/c-elegans-test.yaml --no-replicates --circos-bin-width 10000 --circos-show-chroms I --logging-level INFO --log-file /data/rpbp-predictions-summary.log
Due to the size of the data, we reduce the bin width for the Circos plot. We also need to specify which sequences or chromosomes we want to include (by default, only numbered chromosomes and X/x, Y/y are shown). You now have a new directory analysis with profile_construction and rpbp_predictions output.
Launch any of the web applications with
docker run -p 8050:8050 --volume `pwd`:/data quay.io/biocontainers/rpbp:3.0.1--py310h30d9df9_0 rpbp-profile-construction-dashboard -c /data/c-elegans-test.yaml --host="0.0.0.0"
singularity run --bind `pwd`:/data rpbp.sif rpbp-profile-construction-dashboard -c /data/c-elegans-test.yaml --host="0.0.0.0"
or
docker run -p 8050:8050 --volume `pwd`:/data quay.io/biocontainers/rpbp:3.0.1--py310h30d9df9_0 rpbp-predictions-dashboard -c /data/c-elegans-test.yaml --host="0.0.0.0"
singularity run --bind `pwd`:/data rpbp.sif rpbp-predictions-dashboard -c /data/c-elegans-test.yaml --host="0.0.0.0"
You then have to open a browser page at the correct address, e.g. you see Running on http://127.0.0.1:8050, click on this link, or open a browser page at this address. To navigate the apps is easy, just follow the “hints”. Most items are interactive. Press CTRL+C to quit.
Attention
For the apps only, the configuration file is passed using a (required) named argument -c/--config CONFIG.