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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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Installation and running of METABOLIC docker file #63

Open B-1991-ing opened 2 years ago

B-1991-ing commented 2 years ago

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Dear all,

Thank you very much for developing the docker installation for METABOLIC. My current boss likes it very much and suggested me this paper - METABOLIC: High-throughput profiling of microbial genomes for functional traits, biogeochemistry, and community-scale metabolic networks.

I installed the METABOLIC image on my Mac under the terminal directory - /Users/bing/ through the command line - docker pull tin6150/metabolic:4.0.

I then operated the flollowing Build Commands as below after operating the command line - docker pull tin6150/metabolic:4.0. docker build -t tin6150/base4metabolic -f Dockerfile.base . | tee Dockerfile.base.log WHAT I GOT: [+] Building 0.1s (1/2)
=> [internal] load build definition from Dockerfile.base 0.0s => => transferring dockerfile: 2B 0.0s failed to solve with frontend dockerfile.v0: failed to read dockerfile: open /var/lib/docker/tmp/buildkit-mount033990402/Dockerfile.base: no such file or directory

docker build -t tin6150/perl4metabolic -f Dockerfile.perl . | tee Dockerfile.perl.log WHAT I GOT: [+] Building 0.1s (1/2)
=> [internal] load build definition from Dockerfile.perl 0.0s => => transferring dockerfile: 2B 0.0s failed to solve with frontend dockerfile.v0: failed to read dockerfile: open /var/lib/docker/tmp/buildkit-mount809121847/Dockerfile.perl: no such file or directory

docker build -t tin6150/metabolic -f Dockerfile.metabolic . | tee Dockerfile.log WHAT I GOT: [+] Building 0.1s (1/2)
=> [internal] load build definition from Dockerfile.metabolic 0.0s => => transferring dockerfile: 2B 0.0s failed to solve with frontend dockerfile.v0: failed to read dockerfile: open /var/lib/docker/tmp/buildkit-mount398916690/Dockerfile.metabolic: no such file or directory

docker build -t tin6150/metabolic:4.0 -f Dockerfile.metabolic . | tee Dockerfile.log WHAT I GOT: [+] Building 0.1s (1/2)
=> [internal] load build definition from Dockerfile.metabolic 0.0s => => transferring dockerfile: 2B 0.0s failed to solve with frontend dockerfile.v0: failed to read dockerfile: open /var/lib/docker/tmp/buildkit-mount164655761/Dockerfile.metabolic: no such file or directory

IN ADDITION, under the directory - /Users/bing/METABOLIC, I also run this command line - docker run -v "$(pwd)":/tmp/home --entrypoint "perl" tin6150/metabolic:4.0 /opt/METABOLIC/METABOLIC-G.pl -t 34 -in-gn /Users/bing/Desktop/amplicon_seqs -o /tmp/home/metabolic_out WHAT I GOT:

(base) bing@Bings-MacBook-Pro METABOLIC % docker run -v "$(pwd)":/tmp/home --entrypoint "perl" tin6150/metabolic:4.0 /opt/METABOLIC/METABOLIC-G.pl -t 34 -in-gn /Users/bing/Desktop/amplicon_seqs -o /tmp/home/metabolic_out mkdir: cannot create directory ‘/tmp/home/metabolic_out’: File exists mkdir: cannot create directory ‘/tmp/home/metabolic_out/intermediate_files’: File exists ls: cannot access '/Users/bing/Desktop/amplicon_seqs/.fasta': No such file or directory [2022-03-06 06:00:49] The Prodigal annotation is running... [2022-03-06 06:00:49] The Prodigal annotation is finished ls: cannot access '/Users/bing/Desktop/amplicon_seqs/.faa': No such file or directory sh: 1: cannot create /Users/bing/Desktop/amplicon_seqs/faa.total: Directory nonexistent mv: cannot stat '/Users/bing/Desktop/amplicon_seqs/faa.total': No such file or directory mkdir: cannot create directory ‘/tmp/home/metabolic_out/intermediate_files/Hmmsearch_Outputs’: File exists [2022-03-06 06:00:50] The hmmsearch is running with 34 cpu threads...

Error: Failed to open sequence file /Users/bing/Desktop/amplicon_seqs/total.faa for reading

Error: Failed to open sequence file /Users/bing/Desktop/amplicon_seqs/total.faa for reading

Error: Failed to open sequence file /Users/bing/Desktop/amplicon_seqs/total.faa for reading

Error: Failed to open sequence file /Users/bing/Desktop/amplicon_seqs/total.faa for reading

Error: Failed to open sequence file /Users/bing/Desktop/amplicon_seqs/total.faa for reading

Error: Failed to open sequence file /Users/bing/Desktop/amplicon_seqs/total.faa for reading..........................................

So, my question is I didn't install the docker successfully I think.

I am looking forward your reply.

Best,

Bing Song

ChaoLab commented 2 years ago

Hi Bing, Thank you very much for your interest in our software. Currently, we are not maintaining the docker installation. Instead, we recommend the conda installation approach: https://github.com/AnantharamanLab/METABOLIC/wiki/Installation#anaconda-environment which is much faster and easier. It works well in both Mac and Linux systems.

Chao

B-1991-ing commented 2 years ago

Dear Chao,

Thank you very much for your quick response.

I run the command line - conda env create -f / /Users/bing/Desktop/METABOLIC/METABOLIC_v4.0_env.yml on my Mac under the directory - /Users/bing. WHAT I GOT: SpecNotFound: /Users/bing/Desktop/METABOLIC/METABOLIC_v4.0_env.yml was not found on anaconda.org. You may need to be logged in. Try running: anaconda login

I run the command line - conda env create -f conda env create -f https://github.com/AnantharamanLab/METABOLIC/blob/master/METABOLIC_v4.0_env.yml under the directory - /Users/bing. WHAT I GOT:

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 88, in execute
    spec = specs.detect(name=name, filename=get_filename(args.file), directory=os.getcwd())
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda_env/specs/__init__.py", line 43, in detect
    if spec.can_handle():
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
    self._environment = env.from_file(self.filename)
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda_env/env.py", line 166, in from_file
    return from_yaml(yamlstr, filename=filename)
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda_env/env.py", line 143, in from_yaml
    data = yaml_safe_load(yamlstr)
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 67, in yaml_safe_load
    return yaml.safe_load(string, version="1.2")
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/main.py", line 980, in safe_load
    return load(stream, SafeLoader, version)
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/main.py", line 935, in load
    return loader._constructor.get_single_data()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/constructor.py", line 109, in get_single_data
    node = self.composer.get_single_node()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/composer.py", line 78, in get_single_node
    document = self.compose_document()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/composer.py", line 104, in compose_document
    self.parser.get_event()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/parser.py", line 163, in get_event
    self.current_event = self.state()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/parser.py", line 239, in parse_document_end
    token = self.scanner.peek_token()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 182, in peek_token
    self.fetch_more_tokens()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 282, in fetch_more_tokens
    return self.fetch_value()
  File "/Users/bing/opt/anaconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 651, in fetch_value
    raise ScannerError(
ruamel_yaml.scanner.ScannerError: mapping values are not allowed here
  in "<unicode string>", line 26, column 67:
     ... e" content="{&quot;version&quot;: &quot;4&quot;, &quot;rollouts& ... 
                                         ^ (line: 26)

$ /Users/bing/opt/anaconda3/bin/conda-env create -f https://github.com/AnantharamanLab/METABOLIC/blob/master/METABOLIC_v4.0_env.yml ....................................

What happened there?

Best,

Bing

ChaoLab commented 2 years ago

Did you download the yml file to your server or Mac?

B-1991-ing commented 2 years ago

I think so, as I downloaded https://github.com/AnantharamanLab/METABOLIC/blob/master/METABOLIC_v4.0_env.yml to the directory - /Users/bing/Desktop/METABOLIC on my Mac.

patriciatran commented 2 years ago

In your command try using the path to the yml file on your computer. make sure there are no extra spaces or dashes:

conda create -n /Users/bing/Desktop/METABOLIC/METABOLIC_v4.0_env.yml

B-1991-ing commented 2 years ago

Hi Patricia,

Thank you very much for your reply.

I run the command line - conda create -n /Users/bing/Desktop/METABOLIC/METABOLIC_v4.0_env.yml on my Mac terminal.

WHAT I GOT:

Screenshot 2022-03-08 at 19 56 20

Best,

Bing

patriciatran commented 2 years ago

could you try cd into /Users/bing/Desktop/METABOLIC/ and typing: conda env create -f METABOLIC_v4.0_env.yml and tell me what you get please?

B-1991-ing commented 2 years ago

I changed the directory to /Users/bing/Desktop/METABOLIC/ and run the command line - conda env create -f METABOLIC_v4.0_env.yml.

WHAT I GOT:

Screenshot 2022-03-08 at 20 23 52

I run the command line - conda create -n METABOLIC_v4.0_env.yml. The conda environment is "METABOLIC_v4.0_env.yml" instead of "METABOLIC_v4.0".

WHAT I GOT:

Screenshot 2022-03-08 at 20 25 19
patriciatran commented 2 years ago

ooooh ok. I think the yml file was made for a Linux install -- do we have a way to make it work on mac @ChaoLab ?

B-1991-ing commented 2 years ago

You are right. But, I still downloaded the yml file you uploaded a few minutes ago and run it.

WHAT I GOT

Screenshot 2022-03-08 at 21 14 27