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every time the same error occurs that solving environment killed #67

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HK0911 opened this issue May 10, 2023 · 3 comments
Open

every time the same error occurs that solving environment killed #67

HK0911 opened this issue May 10, 2023 · 3 comments

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@HK0911
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HK0911 commented May 10, 2023

$ conda update -n base -c conda-forge conda -y
conda env create -n tormes-1.3.0 --file tormes-1.3.0.yml
Collecting package metadata (current_repodata.json): done
Solving environment: |
Warning: 2 possible package resolutions (only showing differing packages):

  • conda-forge/noarch::decorator-4.4.2-py_0, conda-forge/noarch::networkx-2.5.1-pyhd8ed1ab_0
  • conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0, conda-forge/noarch::networkx-2.3-pydone

==> WARNING: A newer version of conda exists. <==
current version: 22.9.0
latest version: 23.3.1

Please update conda by running

$ conda update -n base -c conda-forge conda

Package Plan

environment location: /home/hk09/anaconda3

added / updated specs:
- conda

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
bedtools-2.31.0            |       h468198e_0         1.5 MB  bioconda
diff-match-patch-20230430  |     pyhd8ed1ab_0          40 KB  conda-forge
infernal-1.1.4             | pl5321hec16e2b_2         3.4 MB  bioconda
------------------------------------------------------------
                                       Total:         5.0 MB

The following packages will be UPDATED:

bedtools 2.30.0-h468198e_3 --> 2.31.0-h468198e_0 None
diff-match-patch 20200713-pyh9f0ad1d_0 --> 20230430-pyhd8ed1ab_0 None
infernal 1.1.4-pl5321hec16e2b_1 --> 1.1.4-pl5321hec16e2b_2 None

Downloading and Extracting Packages
infernal-1.1.4 | 3.4 MB | ############################################################################# | 100%
bedtools-2.31.0 | 1.5 MB | ############################################################################# | 100%
diff-match-patch-202 | 40 KB | ############################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Retrieving notices: ...working... done
-bash: export: =': not a valid identifier -bash: export: D:wgsrawGTDBTk-mastergtdbtktestsdata=': not a valid identifier
Collecting package metadata (repodata.json): done
Solving environment: - Killed

@HK0911
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HK0911 commented May 10, 2023

conda env create -name tormes-1.3.0 --file tormes-1.3.0.yml
Collecting package metadata (repodata.json): done
Solving environment: - Killed

@biobrad
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biobrad commented Jul 6, 2023

I recommend using Mamba for tormes install now. Conda seems to have problems resolving the environment.

@biobrad
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biobrad commented Jul 6, 2023

Using mamba
We have experienced long times while solving environment by using conda in some cases. If this happens to you, you can install the environment by using Mamba.
To install mamba, please make sure you do so in the "base" environment, as its installation in any other environment is not supported:

conda install mamba -n base -c conda-forge
Once you have mamba installed run:

mamba env create -n tormes-1.3.0 --file tormes-1.3.0.yml

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