Bioconda as a channel depends on Conda Forge and so specifying bioconda as the only channel is incorrect. Instead, a proper specification for using the bioconda channel is
name: freebayes
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- freebayes=1.3.6
See the channel configuration in the Usage section.
Answer from merv on Stack OverflowBioconda as a channel depends on Conda Forge and so specifying bioconda as the only channel is incorrect. Instead, a proper specification for using the bioconda channel is
name: freebayes
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- freebayes=1.3.6
See the channel configuration in the Usage section.
If this helps, I can recreate the issue with:
conda config --set channel_priority strict
mamba env create --file freebayes.yaml
...
Looking for: ['freebayes=1.3.6']
Encountered problems while solving:
- package freebayes-1.3.6-h346b5cb_1 requires htslib >=1.14,<1.15.0a0, but none of the providers can be installed
I can fix it by setting:
conda config --set channel_priority flexible
mamba env create ... # Ok now
Once done, you may want to reset it:
conda config --set channel_priority strict
since at the time of this writing bioconda recommends strict priority.
unable to create conda environment
Cannot.Get.ChopperToRun
python - PackagesNotFoundError: The following packages are not available from current channels (libgcc-ng and libstdcxx-ng) - Stack Overflow
installing qiime2 into windows 11
libgcc-ng, libstdcxx-ng do exist in conda-forge. But they're for Linux only, not for macOS, Windows.
- conda-forge/libgcc-ng
- conda-forge/libstdcxx-ng
These two packages include libraries for gcc. For macOS, install gcc with homebrew. They are contained by the gcc package already.
brew install gcc
As @Simba correctly points out those packages are for linux-* platforms only. If your goal is simply to have a C/C++ compiler (not specifically GCC), consider instead using
conda install -c conda-forge compilers
This will install a platform-appropriate compiler on each platform, and populates the environment variables CC, CXX and GFORTRAN with paths to the respective compilers.
Hi!! I need to install the Proteinortho package (Proteinortho | Anaconda.org) on Miniconda3 to process bioinformatics data. Since the package is only compatible on Linux/MacOS systems (?), I am doing this through Ubuntu WSL. Whenever I run the command to install, this is what happens:
(base) jeannedng@LAPTOP-GE36OC36:~$ conda install bioconda::proteinortho
Channels:
- defaults
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides openmp needed by proteinortho-6.0-py27pl526h9ad8f1e_0
Could not solve for environment specs
The following packages are incompatible
└─ proteinortho =* * is not installable because there are no viable options
├─ proteinortho [6.0|6.0.1|...|6.0b] would require
│ └─ openmp =* *, which does not exist (perhaps a missing channel);
├─ proteinortho 6.0.23 would require
│ └─ liblapacke >=3.8.0,<3.9.0a0 *, which does not exist (perhaps a missing channel);
├─ proteinortho [6.0.24|6.0.25|...|6.0.33] would require
│ └─ liblapacke >=3.8.0,<4.0a0 *, which does not exist (perhaps a missing channel);
├─ proteinortho [6.0.34|6.0.35|...|6.3.5] would require
│ └─ blis =* *, which does not exist (perhaps a missing channel);
└─ proteinortho 6.3.5 would require
└─ libgfortran =* *, which does not exist (perhaps a missing channel).
I apologize if I use terminologies wrong, I am not an IT student nor have any solid background on coding. Let me know what I am doing wrong and what I should be doing. Thank you!