Could you help me to install pyrpipe?

[daschukds]

Hi. I am trying to use pyrpipe for my RNAseq data. I am relatively new to python world. i followed install page (https://pyrpipe.readthedocs.io/en/latest/installation.html) and setting up page (https://pyrpipe.readthedocs.io/en/latest/tutorial/setup.html). Then I wanted to do 'pyrpipe_diagnostic build-tools' and I got this error "pyrpipe_diagnostic: command not found"

I am not sure pyrpipe is installed correctly or the PATH does not have pyrpipe folder. I am testing the system by installing it on an ubuntu 20 OS in my virtual machine. Could you help me?

Thank you.

[urmi-21]

Hi @daschukds can you please confirm if you installed pyrpipe via conda? Can you share the commands that you used?

[daschukds]

Hi urmi-21, Thanks for your reply. I am a beginner to python even though I made a couple of small program with python for my research.

Here is what I did. My setting: windows10 home.

1. I installed VMware and installed Ubuntu (lastest stable version).
2. installed miniconda as you suggested. I followed https://docs.conda.io/en/latest/miniconda.html.
3. conda create -n pyrpipe python=3.8
4. conda activate pyrpipe
5. conda install -c bioconda pyrpipe star=2.7.7a sra-tools=2.10.9 stringtie=2.1.4 trim-galore=0.6.6 orfipy=0.0.3 salmon=1.4.0 It was good upto step 5.

Now. I downloaded yaml file (https://github.com/urmi-21/pyrpipe/blob/master/pyrpipe_environment.yaml) copy the yaml file to home folder in Ubuntu conda env create -f pyrpipe_environment.yaml (downloaded file has yaml exension instead of yml) then I got error as below:

Even though I got the error, i tried to do this line "pyrpipe_diagnostic build-tools" Of course it does not work.

I don't know where to go solve this error.

Could you help me?

Thanks,

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

Traceback (most recent call last):
  File "/home/ds/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1080, in __call__
    return func(*args, **kwargs)
  File "/home/ds/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/ds/miniconda3/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 "/home/ds/miniconda3/lib/python3.9/site-packages/conda_env/specs/__init__.py", line 43, in detect
    if spec.can_handle():
  File "/home/ds/miniconda3/lib/python3.9/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
    self._environment = env.from_file(self.filename)
  File "/home/ds/miniconda3/lib/python3.9/site-packages/conda_env/env.py", line 166, in from_file
    return from_yaml(yamlstr, filename=filename)
  File "/home/ds/miniconda3/lib/python3.9/site-packages/conda_env/env.py", line 143, in from_yaml
    data = yaml_safe_load(yamlstr)
  File "/home/ds/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 67, in yaml_safe_load
    return yaml.safe_load(string, version="1.2")
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/main.py", line 980, in safe_load
    return load(stream, SafeLoader, version)
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/main.py", line 935, in load
    return loader._constructor.get_single_data()
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/constructor.py", line 109, in get_single_data
    node = self.composer.get_single_node()
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/composer.py", line 78, in get_single_node
    document = self.compose_document()
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/composer.py", line 104, in compose_document
    self.parser.get_event()
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/parser.py", line 163, in get_event
    self.current_event = self.state()
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/parser.py", line 239, in parse_document_end
    token = self.scanner.peek_token()
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 182, in peek_token
    self.fetch_more_tokens()
  File "/home/ds/miniconda3/lib/python3.9/site-packages/ruamel_yaml/scanner.py", line 282, in fetch_more_tokens
    return self.fetch_value()
  File "/home/ds/miniconda3/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 191, column 65:
     ... e" content="{&quot;version&quot;: &quot;4&quot;, &quot;rollouts& ... 
                                         ^ (line: 191)

$ /home/ds/miniconda3/bin/conda-env create -f pyrpipe_environment.yaml

environment variables: CIO_TEST= CONDA_AUTO_UPDATE_CONDA=false CONDA_DEFAULT_ENV=pyrpipe CONDA_EXE=/home/ds/miniconda3/bin/conda CONDA_PREFIX=/home/ds/miniconda3/envs/pyrpipe CONDA_PREFIX_1=/home/ds/miniconda3 CONDA_PROMPT_MODIFIER=(pyrpipe) CONDA_PYTHON_EXE=/home/ds/miniconda3/bin/python CONDA_ROOT=/home/ds/miniconda3 CONDA_SHLVL=2 CURL_CA_BUNDLE= PATH=/home/ds/miniconda3/bin:/home/ds/miniconda3/envs/pyrpipe/bin:/home/ds/ miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin: /sbin:/bin:/usr/games:/usr/local/games:/snap/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE= WINDOWPATH=2

 active environment : pyrpipe
active env location : /home/ds/miniconda3/envs/pyrpipe
        shell level : 2
   user config file : /home/ds/.condarc

populated config files : conda version : 4.11.0 conda-build version : not installed python version : 3.9.7.final.0 virtual packages : linux=5.13.0=0 glibc=2.31=0 unix=0=0 archspec=1=x86_64 base environment : /home/ds/miniconda3 (writable) conda av data dir : /home/ds/miniconda3/etc/conda conda av metadata url : None channel URLs : 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/ds/miniconda3/pkgs /home/ds/.conda/pkgs envs directories : /home/ds/miniconda3/envs /home/ds/.conda/envs platform : linux-64 user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.7 Linux/5.13.0-30-generic ubuntu/20.04.3 glibc/2.31 UID:GID : 1000:1000 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve future releases of conda. Would you like conda to send this report to the core maintainers?

[urmi-21]

If you were able to execute step 5 pyrpipe should be installed. No need to create environment using the yaml file. After step 5 run:

pyrpipe --help

You should see the pyrpipe help menu.

[daschukds]

Thank you.

[daschukds]

I have a simple question. I like to use spyder to check my script. I tried to use spyder under pyrpipe. It runs well but it cannot find pyrpipe related files. how can I solve this issue? Thank you.

[urmi-21]

Hi, I think this is because the spyder environment is different than the one containing pyrpipe. You will need to install spyder under the pyrpipe conda environment and then run spyder. This may help https://docs.spyder-ide.org/current/faq.html