conda installation error in hypo
1
0
Entering edit mode
16 months ago
takoyaki ▴ 90

Hi !
I wanted to polish long read by hypo and meet error when installing through conda.
I couldn't solve this problem, so I want to ask you for help. Below are error messages.

(base) $conda install -c bioconda hypo Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with each other: Output in format: Requested package -> Available versions Package zlib conflicts for: hypo -> zlib[version='>=1.2.11,<1.3.0a0'] hypo -> kmc[version='>=3.0'] -> zlib[version='1.2.11.*|1.2.8.*'] Package libstdcxx-ng conflicts for: hypo -> kmc[version='>=3.0'] -> libstdcxx-ng[version='>=7.2.0'] hypo -> libstdcxx-ng[version='>=7.3.0'] Package libgcc-ng conflicts for: hypo -> kmc[version='>=3.0'] -> libgcc-ng[version='>=7.2.0'] hypo -> libgcc-ng[version='>=7.3.0'] Package _libgcc_mutex conflicts for: python=3.7 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main] hypo -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]  I couldn't understand this error message meanings because these doesn't seem to conflict. Also, I checked these packages from conda list command. $ conda list
# packages in environment at /home/user/anaconda3:
#
# Name                    Version                   Build  Channel
zlib                      1.2.11               h7b6447c_3
kmc                       3.1.2rc1             h2d02072_0    bioconda
libstdcxx-ng              9.1.0                hdf63c60_0
libgcc-ng                 9.1.0                hdf63c60_0
_libgcc_mutex             0.1                        main


From these version information, I think all packages meet conditions.
How do you think ? What should I do ??

Below are my environment information.

conda version : 4.8.3
conda-build version : 3.18.11
python version : 3.7.6.final.0
platform : linux-64


anaconda sequencing assembly longread hypo • 963 views
2
Entering edit mode
16 months ago
1. Please remember to use the conda-forge channel as well, we use it in Bioconda for many dependencies.
2. It's highly recommended to create environments for different tools.

.

conda create -n hypo -c conda-forge -c bioconda hypo

0
Entering edit mode

Thanks, Devon. So, it is better to use different virtual environments to avoid these conflict problem.

Please let me ask you one more question. I think that we use a lot of tools in bioinformatics, so will we create many virtual environments, like hypo, busco, flye, medaka ... and so on ?

1
Entering edit mode

Yes, it's good practice to keep tools in separate versioned environments when possible, or at the very least create project-specific environments that you then do not ever change.