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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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problems in installing phyloflash and sortmerna #154

Closed GeonhoCho closed 2 years ago

GeonhoCho commented 2 years ago

Hello,

i created a conda environment and installed phyloflash and sortmerna with the following command.

conda create --prefix ./pf -c bioconda —strict-channel-priority phyloflash sortmerna=2.1b

but ended up with the following error message.

Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libstdcxx-ng conflicts for: sortmerna=2.1b -> libgcc -> libstdcxx-ng[version='>=7.2.0'] phyloflash -> bedtools -> libstdcxx-ng[version='7.2.0.*|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] sortmerna=2.1b -> libstdcxx-ng[version='>=4.9|>=7.3.0']The following specifications were found to be incompatible with your system:

Your installed version is: 2.17

Note that strict channel priority may have removed packages required for satisfiability.

any comments are welcome.

kbseah commented 2 years ago

Please try using mamba instead. See instructions here: https://mamba.readthedocs.io/en/latest/

It is a dropin substitute for conda, and implements a much better environment solver. When I tested your command I got the same error with conda but mamba (v0.1.2) was able to solve the environment.

GeonhoCho commented 2 years ago

Please try using mamba instead. See instructions here: https://mamba.readthedocs.io/en/latest/

It is a dropin substitute for conda, and implements a much better environment solver. When I tested your command I got the same error with conda but mamba (v0.1.2) was able to solve the environment.

It doesn't work, thanks.

kbseah commented 2 years ago

Could you please supply the mamba command line you tried and the error message, as well as the output of conda --version, and the operating system that you are using?

HRGV commented 2 years ago

We have released updated documentation that provides a fix according to our tests.