Nextflow pipeline with docker

federicacitarrella / FusionFlow

FusionFlow is a bioinformatic pipeline that enables the detection of gene fusions from RNA and DNA data.

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Closed federicacitarrella closed 3 years ago

federicacitarrella commented 3 years ago

I tried to install EricScript through Docker and run a nextflow pipeline. I got some conflict errors as shown below.

What should I do? Should I try to install conda instead of using the continuumio/anaconda3 image?

All the useful files were uploaded on GitHub in EricScript_Docker folder. (There are not the RNA sample files)

Bontempogianpaolo1 commented 3 years ago

Uhmm the problem could be related to several RUN command in order to install ericscript... try to combine line 3-5 in an unique RUN instead...

federicacitarrella commented 3 years ago

Nextflow pipeline with docker succeeded. Having Docker installed and downloading the files in "EricScript_Docker_run" directory, you can run:

./build.sh
sudo docker run --rm -it ericscript

Then: ./../nextflow pipeline.nf --in1 '/home/pipelineGeneFusion/sample/SRR064286_1.fastq' --in2 '/home/pipelineGeneFusion/sample/SRR064286_2.fastq'

At the end of the run the following result is shown: