Unable to make skipper environment

[MasaruShimasawa]

Hello,

I couldn't make skipper environment with the following error.
This is after I git-cloned this repository and in the skipper folder.

My OS is OS: macOS Ventura 13.2.1

masarushimasawa@DN0a1f0c0e skipper % conda env create -f installation/skipper_env.yaml
Channels:
 - conda-forge
 - bioconda
 - r
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: - warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
\ warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides requested ucsc-bedgraphtobigwig 455**
  - nothing provides requested star 2.7.10b**
  - nothing provides requested skewer 0.2.2**
  - nothing provides requested samtools 1.17**
  - nothing provides requested homer 4.11**
  - nothing provides requested bedtools 2.31.0**
  - nothing provides requested bioconductor-rtracklayer
  - nothing provides requested bioconductor-genomicranges
  - nothing provides requested bioconductor-fgsea
  - package fastp-0.23.4-h5510893_5 requires libdeflate >=1.20,<1.21.0a0, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ bedtools 2.31.0**  does not exist (perhaps a typo or a missing channel);
├─ bioconductor-fgsea does not exist (perhaps a typo or a missing channel);
├─ bioconductor-genomicranges does not exist (perhaps a typo or a missing channel);
├─ bioconductor-rtracklayer does not exist (perhaps a typo or a missing channel);
├─ fastp 0.23.4**  is installable and it requires
│  └─ libdeflate >=1.20,<1.21.0a0 , which can be installed;
├─ homer 4.11**  does not exist (perhaps a typo or a missing channel);
├─ r-base 4.1.3**  is installable with the potential options
│  ├─ r-base [4.1.3|4.3.0] would require
│  │  └─ libtiff >=4.5.0,<4.6.0a0  but there are no viable options
│  │     ├─ libtiff 4.5.0 would require
│  │     │  └─ libdeflate >=1.17,<1.18.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff [4.5.0|4.5.1] would require
│  │     │  └─ libdeflate >=1.18,<1.19.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff 4.5.0 would require
│  │     │  └─ libdeflate >=1.16,<1.17.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff [4.4.0|4.5.0] would require
│  │     │  └─ libdeflate >=1.14,<1.15.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff 4.5.0 conflicts with any installable versions previously reported;
│  │     └─ libtiff 4.5.1 conflicts with any installable versions previously reported;
│  ├─ r-base [4.1.3|4.3.0|4.3.1] would require
│  │  └─ libtiff >=4.5.1,<4.6.0a0  but there are no viable options
│  │     ├─ libtiff [4.5.0|4.5.1], which cannot be installed (as previously explained);
│  │     └─ libtiff 4.5.1 conflicts with any installable versions previously reported;
│  ├─ r-base [4.1.3|4.3.3] would require
│  │  └─ libtiff >=4.7.0,<4.8.0a0  but there are no viable options
│  │     ├─ libtiff 4.7.0 would require
│  │     │  └─ libdeflate >=1.23,<1.24.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff 4.7.0 would require
│  │     │  └─ libdeflate >=1.21,<1.22.0a0 , which conflicts with any installable versions previously reported;
│  │     └─ libtiff 4.7.0 would require
│  │        └─ libdeflate >=1.22,<1.23.0a0 , which conflicts with any installable versions previously reported;
│  ├─ r-base 4.1.3, which can be installed;
│  ├─ r-base 4.1.3 would require
│  │  └─ libtiff >=4.3.0,<4.5.0a0  but there are no viable options
│  │     ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│  │     ├─ libtiff [4.3.0|4.4.0] would require
│  │     │  └─ libdeflate >=1.10,<1.11.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff 4.3.0 would require
│  │     │  └─ libdeflate >=1.8,<1.9.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff 4.3.0 would require
│  │     │  └─ libdeflate >=1.7,<1.8.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff 4.4.0 would require
│  │     │  └─ libdeflate >=1.12,<1.13.0a0 , which conflicts with any installable versions previously reported;
│  │     ├─ libtiff 4.4.0 would require
│  │     │  └─ libdeflate >=1.13,<1.14.0a0 , which conflicts with any installable versions previously reported;
│  │     └─ libtiff 4.4.0 conflicts with any installable versions previously reported;
│  └─ r-base 4.1.3 would require
│     └─ libtiff >=4.4.0,<4.5.0a0  but there are no viable options
│        ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│        ├─ libtiff [4.3.0|4.4.0], which cannot be installed (as previously explained);
│        ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│        ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│        └─ libtiff 4.4.0 conflicts with any installable versions previously reported;
├─ r-vgam is not installable because there are no viable options
│  ├─ r-vgam 1.1_12 would require
│  │  └─ r-base >=4.3,<4.4.0a0  but there are no viable options
│  │     ├─ r-base [4.1.3|4.3.0], which cannot be installed (as previously explained);
│  │     ├─ r-base [4.1.3|4.3.0|4.3.1], which cannot be installed (as previously explained);
│  │     ├─ r-base [4.3.1|4.3.2|4.3.3] conflicts with any installable versions previously reported;
│  │     └─ r-base [4.1.3|4.3.3], which cannot be installed (as previously explained);
│  └─ r-vgam 1.1_12 would require
│     └─ r-base >=4.4,<4.5.0a0  but there are no viable options
│        ├─ r-base [4.4.0|4.4.1] conflicts with any installable versions previously reported;
│        ├─ r-base 4.4.1 would require
│        │  └─ libdeflate >=1.21,<1.22.0a0 , which conflicts with any installable versions previously reported;
│        ├─ r-base [4.4.1|4.4.2] would require
│        │  └─ libdeflate >=1.22,<1.23.0a0 , which conflicts with any installable versions previously reported;
│        └─ r-base 4.4.2 would require
│           └─ libdeflate >=1.23,<1.24.0a0 , which conflicts with any installable versions previously reported;
├─ samtools 1.17**  does not exist (perhaps a typo or a missing channel);
├─ skewer 0.2.2**  does not exist (perhaps a typo or a missing channel);
├─ star 2.7.10b**  does not exist (perhaps a typo or a missing channel);
└─ ucsc-bedgraphtobigwig 455**  does not exist (perhaps a typo or a missing channel).

[augustboyle]

I was not involved in the conda environment so someone in the Yeo lab would have to address that, but you can attempt to set up the earlier published version that does not rely on a Skipper environment where you can globally or locally install the dependencies: https://github.com/YeoLab/skipper/tree/v1.1.0