parallel-fastq-dump install failed
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Entering edit mode
11 weeks ago
Andy ▴ 20

Good morning,

I am trying to install parallel-fastq-dump but I failed.

And here is what ssh sever say:

conda install parallel-fastq-dump
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- parallel-fastq-dump
Current channels:
 - https://repo.anaconda.com/pkgs/main/linux-64
 - https://repo.anaconda.com/pkgs/main/noarch
 - https://repo.anaconda.com/pkgs/r/linux-64
 - https://repo.anaconda.com/pkgs/r/noarch
 https://conda.anaconda.org/conda-forge/linux-64
 https://conda.anaconda.org/conda-forge/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.

I am wonder what should I do to solve the question?

I also think I could module load the parallel-fast-dump, because I use module load can find this:

module load para
parabricks           parabricks/3.5.0     parabricks/3.6.0-1   parallel             parallel/20190322    parallel/20201122    parallel-fastq-dump

But if I enter I got this error:

module load parallel-fastq-dump 
        Usage: conda activate parallel-fastq-dump
        For more information, see https://github.com/rvalieris/parallel-fastq-dump
parallel-fastq-dump • 335 views
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1
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To add to previous comments, you may want to configure conda to use bioconda once for all (basically, just run conda config commands as shown on the link). Also, I strongly suggest switching to mamba as drop-in replacement for conda install and other conda commands.

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Entering edit mode

did you check this post: link

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Entering edit mode

No, I did not. Thank you, let me take a look.

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1
Entering edit mode

That having said, conda install -c bioconda parallel-fastq-dump.

It even says so on the conda landing page for that tool https://anaconda.org/bioconda/parallel-fastq-dump

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