Unable to create mcclintock environment with mamba

[pramosi1]

Hi!
I'm having trouble installing mcclintock.
I follow all the steps and it gives me an error at the point of creating an environment with mamba:
error libmamba Could not solve for environment specs
The following packages are incompatible
├─ biopython =1.77 * is not installable because it conflicts with any installable versions previously reported;
├─ mamba =0.21.2 * is not installable because it requires
│ └─ conda >=4.8,<4.13.0a0 * but there are no viable options
│ ├─ conda [4.10.0|4.10.1|...|4.9.2] would require
│ │ └─ requests >=2.18.4,<3 * but there are no viable options
│ │ ├─ requests 2.18.4 would require
│ │ │ └─ urllib3 >=1.21.1,<1.22 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests 2.18.4 would require
│ │ │ └─ urllib3 >=1.21.1,<1.23 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.19.0|2.19.1|2.20.0|2.20.1] would require
│ │ │ └─ urllib3 >=1.21.1,<1.24 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.21.0|2.22.0] would require
│ │ │ └─ urllib3 >=1.21.1,<1.25 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.22.0|2.23.0|2.24.0|2.25.0] would require
│ │ │ └─ urllib3 >=1.21.1,(<1.26,(!=1.25.0,!=1.25.1)) *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.25.1|2.26.0|...|2.29.0] would require
│ │ │ └─ urllib3 >=1.21.1,<1.27 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.31.0|2.32.1|2.32.2|2.32.3] would require
│ │ │ └─ urllib3 >=1.21.1,<3 *, which conflicts with any installable versions previously reported;
│ │ └─ requests [2.18.4|2.19.1|...|2.32.3] conflicts with any installable versions previously reported;
│ └─ conda [4.10.0|4.10.1|...|4.9.2] conflicts with any installable versions previously reported;
└─ snakemake =5.32.0 * is not installable because it requires
└─ pygraphviz >=1.5 *, which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

I've tried to troubleshoot it and even talk to tech support at my institution and it's still not working.

[cbergman]

Hi @pramosi1

I have updated the installation instructions to use Miniforge: https://github.com/bergmanlab/mcclintock?tab=readme-ov-file#-installing-condamamba-via-miniforge

Can you please remove your conda/mamba installation and try doing a clean installation of conda/mamba/mcclintock?

Thanks,
Casey

[cbergman]

Any update on this installation problem? If I don't hear anything by the end of next week, I'll assume it's been resolved and close this issue.

[pramosi1]

Any update on this installation problem? If I don't hear anything by the end of next week, I'll assume it's been resolved and close this issue.

Still have the same issue...

(base)$ git clone https://github.com/bergmanlab/mcclintock.git
Cloning into 'mcclintock'...
remote: Enumerating objects: 5404, done.
remote: Counting objects: 100% (1126/1126), done.
remote: Compressing objects: 100% (446/446), done.
remote: Total 5404 (delta 667), reused 992 (delta 651), pack-reused 4278 (from 1)
Receiving objects: 100% (5404/5404), 5.08 MiB | 16.42 MiB/s, done.
Resolving deltas: 100% (3412/3412), done.
Updating files: 100% (212/212), done.
(base)$ cd mcclintock/
(base) $../mcclintock $ mamba env create -f install/envs/mcclintock.yml --name mcclintock
warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.

warning libmamba Please make sure you understand Anaconda Terms of Services.

warning libmamba See: https://legal.anaconda.com/policies/en/
bioconda/linux-64 5.1MB @ 17.5MB/s 0.4s
pkgs/main/noarch 748.3kB @ 3.0MB/s 0.2s
pkgs/main/linux-64 7.6MB @ 11.2MB/s 1.0s
bioconda/noarch 4.8MB @ 3.5MB/s 1.3s
pkgs/r/linux-64 1.6MB @ 6.6MB/s 0.3s
pkgs/r/noarch 2.0MB @ 5.8MB/s 0.4s
anaconda/linux-64 3.6MB @ 9.8MB/s 0.4s
conda-forge/noarch 20.6MB @ 11.2MB/s 2.3s
anaconda/noarch 418.9kB @ 171.6kB/s 0.9s
conda-forge/linux-64 44.3MB @ 16.2MB/s 3.2s

warning libmamba The specification of the environment does not seem solvable in your current setup.
warning libmamba For instance, packages from different channels might be specified,
warning libmamba whilst your current configuration might not allow their resolution.
warning libmamba
warning libmamba If it is the case, you need to either:
warning libmamba - adapt the channel ordering (e.g. by reordering the -c flags in your command line)
warning libmamba - use the flexible channel priority (e.g. using --channel-priority flexible in your command line)
warning libmamba
warning libmamba For reference, see this piece of documentation on channel priority:
warning libmamba https://docs.conda.io/projects/conda/en/stable/user-guide/tasks/manage-channels.html#strict-channel-priority
error libmamba Could not solve for environment specs
The following packages are incompatible
├─ biopython =1.77 * is not installable because it conflicts with any installable versions previously reported;
├─ mamba =0.21.2 * is not installable because it requires
│ └─ conda >=4.8,<4.13.0a0 * but there are no viable options
│ ├─ conda [4.10.0|4.10.1|...|4.9.2] would require
│ │ └─ requests >=2.18.4,<3 * but there are no viable options
│ │ ├─ requests 2.18.4 would require
│ │ │ └─ urllib3 >=1.21.1,<1.22 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests 2.18.4 would require
│ │ │ └─ urllib3 >=1.21.1,<1.23 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.19.0|2.19.1|2.20.0|2.20.1] would require
│ │ │ └─ urllib3 >=1.21.1,<1.24 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.21.0|2.22.0] would require
│ │ │ └─ urllib3 >=1.21.1,<1.25 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.22.0|2.23.0|2.24.0|2.25.0] would require
│ │ │ └─ urllib3 >=1.21.1,(<1.26,(!=1.25.0,!=1.25.1)) *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.25.1|2.26.0|...|2.29.0] would require
│ │ │ └─ urllib3 >=1.21.1,<1.27 *, which conflicts with any installable versions previously reported;
│ │ ├─ requests [2.31.0|2.32.1|2.32.2|2.32.3] would require
│ │ │ └─ urllib3 >=1.21.1,<3 *, which conflicts with any installable versions previously reported;
│ │ └─ requests [2.18.4|2.19.1|...|2.32.3] conflicts with any installable versions previously reported;
│ └─ conda [4.10.0|4.10.1|...|4.9.2] conflicts with any installable versions previously reported;
└─ snakemake =5.32.0 * is not installable because it requires
└─ pygraphviz >=1.5 *, which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

[cbergman]

Did you uninstall you old conda/mamba installation and re-install mamba using miniforge prior to installing mcclintock?