fullama
commented
3 years ago Hmm.. conda issues like these can be notoriously difficult to get a solution to..
Some things to try:
- Update conda
conda update conda - The order of channels matters: https://bioconda.github.io/user/install.html#set-up-channels
- This might not actually help but it might not hurt - remove unused packages/caches
conda clean -a
after all that you could try conda create -n gunc gunc to create and install gunc all in one go
..it could just be that one of the dependencies is just not compatible with the version of linux you are trying to run it on.. Is it an older linux version/older hardware?
you could also try going down the more manual route:
conda create -n gunc
conda activate gunc
conda install diamond=2.0.4 prodigal python
pip install gunc
..this is less safe as pip will install regardless of compatibility but it could work just fine..
Hope that helps.. Let me know how you get on!
hexaquo
ggavelis
Hi!
I can only echo the excitement other posters have for using this tool. But I am having trouble getting the conda installation to work for the latest posted versions (1.0.0 and 1.0.1). I do not have admin privileges on the system I am installing to (it is a cluster environment - GNU/Linux x86_64) so following the exact given instruction fails. Here is what I did instead:
1) I modified my ~.condarc file with the install destination 2) conda create -n gunc -c bioconda 3) conda install -n gunc -c bioconda gunc
This results in the install of v.0.1.2 though.
If I modify step 3 to: conda install -n gunc -c bioconda gunc=1.0.1
Then I just get a lot of errors: 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 six conflicts for: scipy -> mkl-service[version='>=2,<3.0a0'] -> six numpy -> mkl-service[version='>=2,<3.0a0'] -> six pandas -> python-dateutil[version='>=2.7.3'] -> six[version='>=1.5'] plotly -> six plotly -> retrying[version='>=1.3.3'] -> six[version='>=1.7.0']
Package libgcc-ng conflicts for: pandas -> libgcc-ng[version='>=7.2.0|>=7.3.0'] diamond=2.0.4 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0|>=7.3.0'] diamond=2.0.4 -> libgcc-ng[version='>=7.5.0'] prodigal -> libgcc-ng[version='>=7.3.0'] numpy -> libgcc-ng[version='>=7.2.0|>=7.3.0'] numpy -> libopenblas[version='>=0.3.2,<0.3.3.0a0'] -> libgcc-ng[version='>=8.2.0'] plotly -> python -> libgcc-ng[version='>=7.2.0|>=7.3.0'] scipy -> libopenblas[version='>=0.3.2,<0.3.3.0a0'] -> libgcc-ng[version='>=8.2.0'] python[version='>=3.6'] -> libgcc-ng[version='>=7.2.0|>=7.3.0'] requests -> python -> libgcc-ng[version='>=7.2.0|>=7.3.0'] scipy -> libgcc-ng[version='>=7.2.0|>=7.3.0']
Package libstdcxx-ng conflicts for: python[version='>=3.6'] -> libstdcxx-ng[version='>=7.2.0|>=7.3.0'] requests -> python -> libstdcxx-ng[version='>=7.2.0|>=7.3.0'] diamond=2.0.4 -> libstdcxx-ng[version='>=7.5.0'] scipy -> libstdcxx-ng[version='>=7.2.0|>=7.3.0'] numpy -> python[version='>=3.9,<3.10.0a0'] -> libstdcxx-ng[version='>=7.2.0|>=7.3.0'] plotly -> python -> libstdcxx-ng[version='>=7.2.0|>=7.3.0'] pandas -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']
Package _libgcc_mutex conflicts for: scipy -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main] numpy -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main] python[version='>=3.6'] -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main] diamond=2.0.4 -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex=[build=main] pandas -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main] prodigal -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]
Package numpy conflicts for: numpy pandas -> numpy[version='>=1.11.3,<2.0a0|>=1.12.1,<2.0a0|>=1.13.3,<2.0a0|>=1.14.6,<2.0a0|>=1.15.4,<2.0a0|>=1.16.6,<2.0a0|>=1.9.3,<2.0a0|>=1.9'] scipy -> numpy[version='>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16.6,<2.0a0|>=1.15.1,<2.0a0|>=1.9.3,<2.0a0']
Package requests conflicts for: requests plotly -> requests
Package pytz conflicts for: pandas -> pytz[version='>=2017.2'] plotly -> pytz
Package setuptools conflicts for: plotly -> setuptools python[version='>=3.6'] -> pip -> setuptools
Package intel-openmp conflicts for: numpy -> mkl[version='>=2019.4,<2021.0a0'] -> intel-openmp scipy -> mkl[version='>=2019.4,<2021.0a0'] -> intel-openmp
Any advice would be appreciated! Thanks, Craig Herbold