FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
459 stars 149 forks source link

problems installing via conda/mamba #179

Open mawa86 opened 10 months ago

mawa86 commented 10 months ago

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 commented 10 months ago

Hmm, could you raise this issue over that bioconda?