mantis: command not found

[aiguoguo1]

What's wrong during installation?

"
Pressed and indexed 7834 HMMs (7834 names and 7834 accessions).
Models pressed into binary file: /mnt/d/linux/binny/database/hmms/checkm_pf/checkm_filtered_pf.hmm.h3m
SSI index for binary model file: /mnt/d/linux/binny/database/hmms/checkm_pf/checkm_filtered_pf.hmm.h3i
Profiles (MSV part) pressed into: /mnt/d/linux/binny/database/hmms/checkm_pf/checkm_filtered_pf.hmm.h3f
Profiles (remainder) pressed into: /mnt/d/linux/binny/database/hmms/checkm_pf/checkm_filtered_pf.hmm.h3p
mantis: command not found
"
there is no command called "mantis setup -mc ..."

Could you please tell me what software has this command "mantis"???

[ohickl]

Hi,
I was unable to reproduce this running the setup with:

git clone https://github.com/a-h-b/binny.git --branch v2.2.15
cd binny
./binny -i config/config.init.yaml 

Note that for the test run and subsequent runs you would need to to the following, as some things out ouf our hands broke. So after successful setup you will have to run:

# Set binny conda environment path
CONDA_SOURCE="/path/to/binny/conda/envs"
# Fix Snakemake
conda activate ${CONDA_SOURCE}/snakemake_env
conda install -c bioconda snakemake=7.16.0
# Fix hdbscan
for i in ${CONDA_SOURCE}/*.yaml; do
  env_name=$(head -n 1 ${i} | cut -d' ' -f2)
  if [[ ${env_name} == 'binny_linux' ]]; then
    binny_env=${i%.yaml}
    echo "Loading binny env from: ${binny_env}"
  fi
done
conda activate ${binny_env}
conda install -c conda-forge hdbscan=0.8.29
conda activate base

Now it should work fine.
Although i would anyway go with the latest version from the main repo.

Hope that helps. Let me know, if there's further problems.

Best

Oskar