Answers.Body: <p>Could you download it from <code>conda</code> and try again? Its here, <a href="https://docs.conda.io/en/main/miniconda.html" rel="nofollow noreferrer">https://docs.conda.io/en/main/miniconda.html</a></p>
  <p>Then,</p>
  <pre><code>conda create --name myenv
  conda activate myenv
  conda install -c bioconda cnvkit
  cnvkit batch /path/to/my/folder/with/bams/*.bam --normal --targets ${bed_file} --fasta path/to/my/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --output-reference /path/to/my/CD_BATCH1_reference.cnn --output-dir /path/to/my/Group_1 --scatter 
  </code></pre>
  <p>The path to the file is not used, the command is simply <code>cnvkit</code>
  This avoids all the privilege stuff and ensures you're running a virtual environment to protect your system Python.</p>
  <hr />
  <p>To address the comments. &quot;conda&quot; is slow and doesn't ever load.</p>
  <p>There is an alternative to conda called <strong>mamba</strong>, this is fast and designed to address this exact issue. I have never needed to use it so the following is a rough guide only.</p>
  <p>Download and install via</p>
  <pre><code>conda create --name myenv
  conda activate myenv
  conda install -c conda-forge mamba
  </code></pre>
  <p>The documentation is here, <a href="https://mamba.readthedocs.io/en/latest/user_guide/mamba.html" rel="nofollow noreferrer">https://mamba.readthedocs.io/en/latest/user_guide/mamba.html</a></p>
  <p>I've never used it but the idea is ...</p>
  <pre><code>mamba create -n mambaenv &lt;list of packages&gt;
  mamba activate mambaenv
  </code></pre>
  <p>The list of packages could be left blank for now, then,</p>
  <pre><code>mamba install &quot;Python&gt;=3.10.0&quot; numpy pandas pathlib
  mamba install cnvkit # SEE NOTE
  </code></pre>
  <p>Can also do</p>
  <pre><code>mamba install -n mambaenv cnvkit
  </code></pre>
  <p><strong>NOTE</strong> cnvkit exists strictly in -c bioconda. You do not seem to search and install via channels in mamba</p>
  <p>You search for a package and its dependencies via</p>
  <pre><code>mamba repoquery search cnvkit
  mamba repoquery depends -a cnvkit
  </code></pre>
  <p>It is important to place a virtual environment between the system Python and package Python (don't want a system corruption). More to the question, this would solve all the permission problems without changing your system in anyway (kinda important).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-12T13:37:19.990Z
Answers.Text: I did try this before and I tried it again now but for whatever reason I get `Solving environment: failed with initial frozen solve. Retrying with flexible solve.` over and over again. It never works though for the command `conda install -c bioconda cnvkit`.
Answers.UserDisplayName: Indira
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-12T13:52:37.660Z
Answers.Text: Okay @Indira thanks. Addressed above
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-12T15:05:28.470Z
Answers.Text: "I have never needed to use it" you lucky so-and-so! We regular joes need to stick to mamba if we need conda environments solved in one human lifetime.
Answers.UserDisplayName: Ram RS
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-12T17:33:00.013Z
Answers.Text: @RamRS this is funny. I suggest the reason is that "Regular Joses" (pronounced Hosays) where I am, don't use conda. "Regular Joes" where you are, all use conda. Thus your server always times out. :-)
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-11T20:33:54.967Z
Answers.LastActivityDate: 2023-05-12T14:29:51.863Z
Answers.LastEditDate: 2023-05-12T14:29:51.863Z
Answers.UserDisplayName: M__
Body: <p>I am trying to run some code for my colleague in bash</p>
  <pre><code>/path/to/cnvkit.py batch /path/to/my/folder/with/bams/*.bam \
    --normal --targets ${bed_file} \
    --fasta path/to/my/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta \
    --output-reference /path/to/my/CD_BATCH1_reference.cnn \
    --output-dir /path/to/my/Group_1 --scatter
  </code></pre>
  <p>however, I keep getting this truly peculiar error</p>
  <pre><code>Traceback (most recent call last):
    File &quot;/path/to/cnvkit.py&quot;, line 4, in &lt;module&gt;
      from . import commands
  ImportError: cannot import name 'commands' from '__main__' (/path/to/cnvkit.py)
  </code></pre>
  <p><strong>Attempt 1</strong></p>
  <p>I checked if the path was correct and multiple times I found that it was correct. It did not change the error.</p>
  <p><strong>Attempt 2</strong></p>
  <p>Perhaps I need to <code>chmod +x *</code> everything in the CNV kit directory and that will help. It did not change the error.</p>
  <p>Why is this error occurring? How do I solve this issue?</p>
  
Tags: <bash><cnv>
Title: CNV Kit ` from . import commands ImportError: cannot import name 'commands' from '__main__'`
ThreadText: # CNV Kit ` from . import commands ImportError: cannot import name 'commands' from '__main__'`
  
  (Asked by: username_0 on 2023-05-11)
  
  I am trying to run some code for my colleague in bash
  
  ```
  /path/to/cnvkit.py batch /path/to/my/folder/with/bams/*.bam \
    --normal --targets ${bed_file} \
    --fasta path/to/my/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta \
    --output-reference /path/to/my/CD_BATCH1_reference.cnn \
    --output-dir /path/to/my/Group_1 --scatter
  
  ```
  
  however, I keep getting this truly peculiar error
  
  ```
  Traceback (most recent call last):
    File "/path/to/cnvkit.py", line 4, in <module>
      from . import commands
  ImportError: cannot import name 'commands' from '__main__' (/path/to/cnvkit.py)
  
  ```
  
  **Attempt 1**
  
  I checked if the path was correct and multiple times I found that it was correct. It did not change the error.
  
  **Attempt 2**
  
  Perhaps I need to `chmod +x *` everything in the CNV kit directory and that will help. It did not change the error.
  
  Why is this error occurring? How do I solve this issue?
  
  **Tags:** bash, cnv
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-05-11. Score: 1 | Accepted answer
  
  Could you download it from `conda` and try again? Its here, <https://docs.conda.io/en/main/miniconda.html>
  
  Then,
  
  ```
  conda create --name myenv
  conda activate myenv
  conda install -c bioconda cnvkit
  cnvkit batch /path/to/my/folder/with/bams/*.bam --normal --targets ${bed_file} --fasta path/to/my/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --output-reference /path/to/my/CD_BATCH1_reference.cnn --output-dir /path/to/my/Group_1 --scatter 
  
  ```
  
  The path to the file is not used, the command is simply `cnvkit`
  This avoids all the privilege stuff and ensures you're running a virtual environment to protect your system Python.
  
  ---
  
  To address the comments. "conda" is slow and doesn't ever load.
  
  There is an alternative to conda called **mamba**, this is fast and designed to address this exact issue. I have never needed to use it so the following is a rough guide only.
  
  Download and install via
  
  ```
  conda create --name myenv
  conda activate myenv
  conda install -c conda-forge mamba
  
  ```
  
  The documentation is here, <https://mamba.readthedocs.io/en/latest/user_guide/mamba.html>
  
  I've never used it but the idea is ...
  
  ```
  mamba create -n mambaenv <list of packages>
  mamba activate mambaenv
  
  ```
  
  The list of packages could be left blank for now, then,
  
  ```
  mamba install "Python>=3.10.0" numpy pandas pathlib
  mamba install cnvkit # SEE NOTE
  
  ```
  
  Can also do
  
  ```
  mamba install -n mambaenv cnvkit
  
  ```
  
  **NOTE** cnvkit exists strictly in -c bioconda. You do not seem to search and install via channels in mamba
  
  You search for a package and its dependencies via
  
  ```
  mamba repoquery search cnvkit
  mamba repoquery depends -a cnvkit
  
  ```
  
  It is important to place a virtual environment between the system Python and package Python (don't want a system corruption). More to the question, this would solve all the permission problems without changing your system in anyway (kinda important).
  
  > **Comments:**
  > **username_0**: I did try this before and I tried it again now but for whatever reason I get `Solving environment: failed with initial frozen solve. Retrying with flexible solve.` over and over again. It never works though for the command `conda install -c bioconda cnvkit`.  
  > **username_1**: Okay @username_0 thanks. Addressed above  
  > **username_2**: "I have never needed to use it" you lucky so-and-so! We regular joes need to stick to mamba if we need conda environments solved in one human lifetime.  
  > **username_1**: @username_2 this is funny. I suggest the reason is that "Regular Joses" (pronounced Hosays) where I am, don't use conda. "Regular Joes" where you are, all use conda. Thus your server always times out. :-)  
  
  ---
  
  