problems installing via conda/mamba

[mawa86]

Relatively new to everything that isn't Windows I'm afraid.. can anyone help me out here?

(kraken2) martin@martin-VirtualBox:~$ mamba install -c bioconda trim-galore

Looking for: ['trim-galore']

bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
warning  libmamba Cache file "/home/martin/miniconda3/pkgs/cache/47929eba.json" was modified by another program
pkgs/main/linux-64 (check zst)                     Checked  0.1s
warning  libmamba Cache file "/home/martin/miniconda3/pkgs/cache/3e39a7aa.json" was modified by another program
pkgs/main/noarch (check zst)                       Checked  0.0s
warning  libmamba Cache file "/home/martin/miniconda3/pkgs/cache/2ce54b42.json" was modified by another program
pkgs/r/linux-64 (check zst)                        Checked  0.0s
warning  libmamba Cache file "/home/martin/miniconda3/pkgs/cache/4ea078d6.json" was modified by another program
pkgs/r/noarch (check zst)                          Checked  0.0s
pkgs/main/noarch                                   697.5kB @ 305.7kB/s  2.3s
pkgs/r/noarch                                        1.7MB @ 400.1kB/s  4.4s
pkgs/r/linux-64                                      1.5MB @ 339.9kB/s  4.5s
pkgs/main/linux-64                                   5.4MB @   1.0MB/s  5.4s

Pinned packages:
  - python 3.9.*


warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
└─ trim-galore is installable with the potential options
   ├─ trim-galore [0.4.1|0.4.5|...|0.6.9] would require
   │  └─ cutadapt with the potential options
   │     ├─ cutadapt [1.10|1.11|...|1.9.1] would require
   │     │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
   │     ├─ cutadapt [1.10|1.11|...|1.9.1] would require
   │     │  └─ python 3.4* , which does not exist (perhaps a missing channel);
   │     ├─ cutadapt [1.10|1.11|...|1.9.1] would require
   │     │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
   │     ├─ cutadapt [1.13|1.14|...|2.6] would require
   │     │  └─ python [3.6* |>=3.6,<3.7.0a0 ], which can be installed;
   │     ├─ cutadapt [1.18|2.0|...|2.6] would require
   │     │  └─ python >=3.7,<3.8.0a0 , which can be installed;
   │     ├─ cutadapt [2.10|2.9|...|3.5] would require
   │     │  └─ python_abi 3.6.* *_cp36m, which does not exist (perhaps a missing channel);
   │     ├─ cutadapt [2.10|2.9|...|4.0] would require
   │     │  └─ python_abi 3.7.* *_cp37m, which does not exist (perhaps a missing channel);
   │     ├─ cutadapt [2.10|3.0|...|4.0] would require
   │     │  └─ python_abi 3.8.* *_cp38, which does not exist (perhaps a missing channel);
   │     ├─ cutadapt [2.7|2.8] would require
   │     │  └─ xopen >=0.8.4 , which does not exist (perhaps a missing channel);
   │     ├─ cutadapt [3.3|3.4|...|4.0] would require
   │     │  └─ python_abi 3.9.* *_cp39, which does not exist (perhaps a missing channel);
   │     └─ cutadapt [4.1|4.2|4.3|4.4|4.5] would require
   │        └─ libgcc-ng >=12 , which does not exist (perhaps a missing channel);
   └─ trim-galore [0.4.1|0.4.3|0.4.4|0.4.5] would require
      └─ perl 5.22.0* , which does not exist (perhaps a missing channel).

if I try to install cutadapt first i get a similar error. this is on a Ubuntu 20 machine with a python=3.9 conda environment

thanks for any help
M

[FelixKrueger]

Hmm, could you raise this issue over that bioconda?