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chsmiss / ATAC-amp

Searching for co-amplified regions on the genome from ATAC-seq data
MIT License
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Encountered an error while configuring the environment #1

Open Maple-sakura opened 11 months ago

Maple-sakura commented 11 months ago

When configuring the mamba environment, although the 'interval' module has been installed, an error 'module 'interval' has no attribute 'Interval'' occurs during runtime. I am using Python version 3.7. I infrequently use Python, and I suspect there might be a mismatch in Python or interval versions compared to the author's. Is it possible to ask you to export the analysis environment in YAML format, such as config.yaml?

chsmiss commented 11 months ago

Hi, thanks for your question. We have test run this on two machines with different versions of python, one with python version 3.7.12 and imported the following modules and versions: pysam 0.21.0 networkx 2.6.3 psutil 5.9.4 interval 1.0.0 The other is using python 3.9.7 with the following dependent modules and versions.  psutil 5.9.0  networkx 3.0  interval 1.0.0  pysam 0.17.0  If it's not due to the version, please provide us with more detailed information about the error report and we'll be happy to fix it for you.

------------------ 原始邮件 ------------------ 发件人: "chsmiss/ATAC-amp" @.>; 发送时间: 2023年11月24日(星期五) 下午3:52 @.>; @.***>; 主题: [chsmiss/ATAC-amp] Encountered an error while configuring the environment (Issue #1)

When configuring the mamba environment, although the 'interval' module has been installed, an error 'module 'interval' has no attribute 'Interval'' occurs during runtime. I am using Python version 3.7. I infrequently use Python, and I suspect there might be a mismatch in Python or interval versions compared to the author's. Is it possible to ask you to export the analysis environment in YAML format, such as config.yaml?

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GislaineCurty commented 7 months ago

Hi,

Could you please provide detailed instructions on the installation process? I've encountered some errors during installation using conda environment, python 3.4 , such as with interval package:

python AtacAmp.py -h Traceback (most recent call last): File "AtacAmp.py", line 10, in import interval ImportError: No module named 'interval'

conda install interval Channels:

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

conda search -f interval Loading channels: done No match found for: interval. Search: interval

Thank you!

chsmiss commented 7 months ago

Hi， The interval module does not support conda installation at this time.I suggest you install it with pip intall interval，the python versions I use are 3.7 and 3.12, both are fine.Try it out and contact me if you have any questions.

Chenhansen

---Original--- From: @.> Date: Wed, Mar 27, 2024 03:01 AM To: @.>; Cc: @.**@.>; Subject: Re: [chsmiss/ATAC-amp] Encountered an error while configuring theenvironment (Issue #1)

Hi,

Could you please provide detailed instructions on the installation process? I've encountered some errors during installation using conda environment, python 3.4 , such as with interval package:

python AtacAmp.py -h Traceback (most recent call last): File "AtacAmp.py", line 10, in import interval ImportError: No module named 'interval'

conda install interval Channels:

bioconda

conda-forge

defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

interval

Current channels:

https://conda.anaconda.org/bioconda

https://conda.anaconda.org/conda-forge

defaults

To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org
and use the search bar at the top of the page.

conda search -f interval Loading channels: done No match found for: interval. Search: interval

Thank you!

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