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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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Issue with install_conda_env.sh #162

Closed mhayes8520 closed 4 years ago

mhayes8520 commented 4 years ago

Describe the bug I'm trying to install the conda environment on Stanford Sherlock following the steps here (https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/e2a698d0dcc3d7b16ac8b9dc86d2f9097a35f0b8/docs/install_conda.md), and the script keeps failing at line 15 for some reason. I've followed the previous instructions correctly I think, so I'm not sure what to do. I have copied the error log below

OS/Platform

Caper configuration file Paste contents of ~/.caper/default.conf.

Input JSON file Paste contents of your input JSON file.

Error log conda 4.8.2 === Installing pipeline's Conda environments === Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: | chip-seq-pipeline2/scripts/install_conda_env.sh: line 15: 60721 Killed conda create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y -c defaults -c r -c bioconda -c conda-forge

$ caper debug [WORKFLOW_ID_OR_METADATA_JSON_FILE]
leepc12 commented 4 years ago 
60721 Killed conda

Your job was killed by the cluster. Please do it on a compute node. To log-in on a compute node, use sbatch or Sherlock's special command sdev. Check sdev -h for details.

$ sdev -t SOME_LONG_TIME
mhayes8520 commented 4 years ago

Gotcha, I'll try that. Thanks!