Installation in conda

[thierryjanssens]

Hi,

upon an attempt to install basta in conda I go the following error. The yaml file seems to be badly interpreted. $ wget https://github.com/timkahlke/BASTA/blob/master/environment_linux.yml $ conda env create -f environment_linux.yml

...

$ /data/anaconda3/bin/conda-env create -f ./environment_linux.yml

Traceback (most recent call last):
  File "/data/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 640, in conda_exception_handler
    return_value = func(*args, **kwargs)
  File "/data/anaconda3/lib/python3.6/site-packages/conda_env/cli/main_create.py", line 78, in execute
    directory=os.getcwd())
  File "/data/anaconda3/lib/python3.6/site-packages/conda_env/specs/__init__.py", line 20, in detect
    if spec.can_handle():
  File "/data/anaconda3/lib/python3.6/site-packages/conda_env/specs/yaml_file.py", line 14, in can_handle
    self._environment = env.from_file(self.filename)
  File "/data/anaconda3/lib/python3.6/site-packages/conda_env/env.py", line 80, in from_file
    return from_yaml(yamlstr, filename=filename)
  File "/data/anaconda3/lib/python3.6/site-packages/conda_env/env.py", line 68, in from_yaml
    data = yaml.load(yamlstr)
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/main.py", line 75, in load
    return loader.get_single_data()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/constructor.py", line 60, in get_single_data
    node = self.get_single_node()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/composer.py", line 53, in get_single_node
    document = self.compose_document()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/composer.py", line 76, in compose_document
    self.get_event()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/parser.py", line 136, in get_event
    self.current_event = self.state()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/parser.py", line 215, in parse_document_end
    token = self.peek_token()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/scanner.py", line 144, in peek_token
    self.fetch_more_tokens()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/scanner.py", line 239, in fetch_more_tokens
    return self.fetch_value()
  File "/data/anaconda3/lib/python3.6/site-packages/ruamel_yaml/scanner.py", line 598, in fetch_value
    self.get_mark())
ruamel_yaml.scanner.ScannerError: mapping values are not allowed here
  in "<unicode string>", line 323, column 24:
      <!-- blob contrib key: blob_contributors:v21:0b8a2db9 ...

Regards,

Thierry

[thierryjanssens]

Has been solved, since the problem was identified.
wget downloaded the html page instead of the yaml.

[timkahlke]

Hi Thierry, Was just looking into it but good that you solved it. Hope the rest works. Cheers, Tim

[thierryjanssens]

Hi Tim,

after having executed

$conda env create -f environment_linux.yml -n basta

all the dependencies from the yaml were installed the environment, but no basta executable was found in the environments bin folder. Maybe I have overlooked something?

Cheers,

Thierry

[maxibor]

Hi Thierry, The conda environment is just for the dependancies, you still need to git clone and cd to the Basta bin directory. AFAIK, Basta is not (yet) distributed as a package

[nick-youngblut]

Sorry to hit up an old issue, but will there be a pypi and/or conda release of of BASTA any time soon? My research lab tries to only use software that can be installed and maintained with a package manager (preferably conda). This helps increase bioinformatics analysis reproducibility, which is sadly still often lacking for many studies.

[timkahlke]

Fair enough. I will try to free up some time in the next weeks and look into it.

[timkahlke]

Hi all, Just in case it's still of interest: I re-wrote some functions and also build a conda repo. BASTA plus dependencies can now be installed completely using conda:

conda -c bioconda -c bnoon -c timkahlke basta

Hope it works

[nick-youngblut]

That's great! Thanks for creating it!