Example JSON not working

[lcamillo]

Describe the bug

I have just cloned and installed the pipeline using conda, and caper using pip. However, I cannot run the example JSON. Any help would be much appreciated!

OS/Platform

• OS/Platform: Linux (Brown's CS cluster)
• Conda version: 4.10.3
• Pipeline version: 1.9.0
• Caper version: 1.6.3

Caper configuration file

Input JSON file

https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json

Troubleshooting result

And so on.

[leepc12]

This looks like a Conda issue. How did you install Conda? Did you use mamba?
Please uninstall the environment and try without mamba

$ scripts/uninstall_conda_env.sh
$ scripts/install_conda_env.sh # do not add mamba here

Installing without mamba can take long.
If this method doesn't work then try to use docker or singularity methods.

[lcamillo]

I installed Conda through Miniconda3 using the guide provided. I had used mamba to install the pipeline but even without it the same error occurs (undefined symbol ...).

Is there any short guide to use the ENCODE pipeline with docker or singularity?

[leepc12]

Please try to manually re-install bowtie2 (latest) in your Conda environemnt

$ source activate encode-chip-seq-pipeline
$ which bowtie2 # check if bowtie2 binaries are under the environment bin/ folder
$ bowtie2 --version
$ conda uninstall bowtie2
$ conda install bowtie2
$ bowtie2 --version # check version after manual installation

Most HPC clusters do not support docker so if you are working on an HPC try with singularity. If you are working locally on your computer then install docker and simply add --docker to caper run/submit command line.

For HPCs,

$ singularity --version # check if singularity binary exists
$ caper run/submit chip.wdl ... --singularity # caper will automatically parse the singularity image of the pipeline from WDL