kenibrewer
commented
6 months ago I modified the Dockerfile to isolate the failing command into it's own run block and got the following error.
> [ 9/11] RUN mamba install -y python=3.9 gxx_linux-64 bowtie bowtie2 samtools bedtools cutadapt viennarna rnastructure:
16.47
16.47 Looking for: ['python=3.9', 'gxx_linux-64', 'bowtie', 'bowtie2', 'samtools', 'bedtools', 'cutadapt', 'viennarna', 'rnastructure']
16.47
16.47 Could not solve for environment specs
16.47 The following packages are incompatible
16.47 ├─ python 3.9** is requested and can be installed;
16.47 └─ truststore is not installable because there are no viable options
16.47 ├─ truststore [0.7.0|0.8.0] would require
16.47 │ └─ python >=3.10 but there are no viable options
16.47 │ ├─ python [3.10.0|3.10.1|...|3.10.9] conflicts with any installable versions previously reported;
16.47 │ ├─ python [3.11.0|3.11.1|...|3.11.8] conflicts with any installable versions previously reported;
16.47 │ ├─ python [3.12.0|3.12.1|3.12.2] conflicts with any installable versions previously reported;
16.47 │ └─ python 3.12.0rc3 would require
16.47 │ └─ _python_rc, which does not exist (perhaps a missing channel);
16.47 ├─ truststore 0.8.0 would require
16.47 │ └─ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported;
16.47 ├─ truststore 0.8.0 would require
16.47 │ └─ python >=3.11,<3.12.0a0 , which conflicts with any installable versions previously reported;
16.47 └─ truststore 0.8.0 would require
16.47 └─ python >=3.12,<3.13.0a0 , which conflicts with any installable versions previously reported.Looking back at the Dockerfile dependencies, I think the failure was probably introduced by a new version of Miniforge/Mambaforge being released here.
The simplest solution is probably simply to change the pinned version of python in the Dockerfile from 3.9 to 3.10.
See log for details.