Conflicts while running scripts/install_conda_env.sh

[agduncan94]

Describe the bug

When running the install_conda_env.sh script to setup the conda environments, there are many conflicts that are found, causing the install to fail.

It seems to be the encd-chip and encd-chip-spp failing. The encd-chip-macs2 environment installs fine.

conda create -n encd-chip --file ${SH_SCRIPT_DIR}/requirements.txt \
  --override-channels -c bioconda -c defaults -y

...

conda create -n encd-chip-spp --file ${SH_SCRIPT_DIR}/requirements.spp.txt \
  --override-channels -c r -c bioconda -c defaults -y

OS/Platform

• OS/Platform: Ubuntu 20.04
• Conda version: 4.13.0
• Pipeline version: v2.2.0
• Caper version: 2.2.2

Caper configuration file

Paste contents of ~/.caper/default.conf.

backend=local

# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=

cromwell=/home/andrew/.caper/cromwell_jar/cromwell-82.jar
womtool=/home/andrew/.caper/womtool_jar/womtool-82.jar

Troubleshooting result

Here is the beginning output from trying to install encd-chip-spp

Wed 17 Aug 2022 11:50:30 AM EDT: 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: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
...

Here is the full output for trying to install encd-chip-spp
failed.chip.pipeline.install.conda.txt

[Al-Murphy]

Having the same issue with the same set up:

OS/Platform: Ubuntu 20.04
Pipeline version: 2.2.0
Caper version: 2.2.2
Conda v4.13.0

[Al-Murphy]

Just to add a little to this, inspecting the install script, the following conda env will create without issue

conda create -n encd-chip-macs2 --file ${SH_SCRIPT_DIR}/requirements.macs2.txt \
  --override-channels -c bioconda -c defaults -y

but the two below fail for me:

conda create -n encd-chip --file ${SH_SCRIPT_DIR}/requirements.txt \
  --override-channels -c bioconda -c defaults -y

conda create -n encd-chip-spp --file ${SH_SCRIPT_DIR}/requirements.spp.txt \
  --override-channels -c r -c bioconda -c defaults -y

[leepc12]

We will make a fix for this soon. Until then please install Singularity or Docker and use --singularity or --docker method.