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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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Installation problem #118

Closed anilchauhanhp9 closed 1 year ago

anilchauhanhp9 commented 1 year ago

The program failed to install using METABOLIC_v4.0_env.yml file First it showed the error "CondaValueError: Invalid environment name: '/slowdata/yml_environments/METABOLIC_v4.0' Characters not allowed: {'#', ':', '/', ' '}" After removing "/slowdata/yml_environments/" from the yml file it showed following issues Found conflicts! Looking for incompatible packages. It showed a number of conflicts during checking My conda details are as following active environment : base active env location : /home/ham/anaconda3 shell level : 1 user config file : /home/ham/.condarc populated config files : /home/ham/.condarc conda version : 22.9.0 conda-build version : 3.22.0 python version : 3.9.13.final.0 virtual packages : linux=5.4.0=0 glibc=2.31=0 unix=0=0 archspec=1=x86_64 base environment : /home/ham/anaconda3 (writable) conda av data dir : /home/ham/anaconda3/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/ham/anaconda3/pkgs /home/ham/.conda/pkgs envs directories : /home/ham/anaconda3/envs /home/ham/.conda/envs platform : linux-64 user-agent : conda/22.9.0 requests/2.28.1 CPython/3.9.13 Linux/5.4.0-132-generic ubuntu/20.04.5 glibc/2.31 UID:GID : 1000:1000 netrc file : None offline mode : False Please help

ChaoLab commented 1 year ago

Hi, there are indeed some software and package version conflicts when setting up the conda environment. Now, I have tested the following commands, and they work well in my server:

conda create -n METABOLIC_v4.0 python=3.8
conda activate METABOLIC_v4.0

# Install perl, bioperl, and perl modules (mamba here would be faster than conda and you will need to install mamba previously in your server. While, you can still replace mamba by conda)
mamba install perl=5.22.0 perl-bioperl perl-data-dumper perl-posix perl-getopt-long perl-statistics-descriptive perl-carp perl-file-spec perl-file-path perl-parallel-forkmanager

# Install R and R packages
mamba install -c conda-forge r-base r-tidyverse r-ggraph r-ggthemes r-ggalluvial r-ggraph r-openxlsx r-pdftools

# Install dependent software within conda environment
mamba install sambamba bamtools coverm diamond bowtie2 gdown

# Install GTDB-Tk v2.1.0 and use GTDB release 207_v2 as the reference database
mamba install gtdbtk=2.1.0 # Installing GTDB-Tk should be placed in the last step, otherwise, it will be automatically downgraded in order to install other packages
conda env config vars set GTDBTK_DATA_PATH="/slowdata/databases/GTDBTK_DB/release207/release207_v2" # Here, the address to the directory of GTDB release 207_v2 should be changed to your own address
# To make your changes to GTDB reference database take effect, please reactivate your environment

In addition, I also updated the yml file accordingly. You can also try the new yml file

anilchauhanhp9 commented 1 year ago

Hi, I have installed the program as suggested and now it's working fine. Thank you