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conda tophat installation error
bioinfo@bioinfo:~$ conda install -c bioconda tophat
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - tophat

Current channels:

  - https://conda.anaconda.org/bioconda/linux-32
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/default/linux-32
  - https://conda.anaconda.org/default/noarch
  - https://conda.anaconda.org/r/linux-32
  - https://conda.anaconda.org/r/noarch
  - https://repo.anaconda.com/pkgs/main/linux-32
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-32
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-32
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-32
  - https://repo.anaconda.com/pkgs/pro/noarch
  - https://conda.anaconda.org/conda-forge/linux-32
  - 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.

Please suggest how to install package and resolve this problem.

Thank you.

python anaconda
• 5,588 views • link
updated by finswimmer finswimmer • written by amitunited0532 • amitunited0532

Please don't use TopHat for any new projects. There are many current programs that are much better suited for RNAseq. STAR, BBMap, HISAT2 to name a few.

• 0 views • link
written by GenoMax GenoMax

I was try to install Hisat2 but it shows same error.

bioinfo@bioinfo:~$ conda install -c bioconda hisat2 
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - hisat2

Current channels:

  - https://conda.anaconda.org/bioconda/linux-32
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/default/linux-32
  - https://conda.anaconda.org/default/noarch
  - https://conda.anaconda.org/r/linux-32
  - https://conda.anaconda.org/r/noarch
  - https://repo.anaconda.com/pkgs/main/linux-32
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-32
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-32
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-32
  - https://repo.anaconda.com/pkgs/pro/noarch
  - https://conda.anaconda.org/conda-forge/linux-32
  - 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.
• 0 views • link
updated by finswimmer finswimmer • written by amitunited0532 • amitunited0532

Go for a faster aligner like Hisat2, Star etc.

• 0 views • link
written by Arup Ghosh Arup Ghosh

Can I run STAR on normal computer with 4GB RAM, 500GB HDD?

• 0 views • link
written by amitunited0532 • amitunited0532

Only if the genome you're using is tiny. Even hisat2 may run into issues on a small computer like that.

• 0 views • link
written by Devon Ryan Devon Ryan

Hate to say this but if that is all you have you should stop now and find alternate hardware with better resources. What genome are you working with?

• 0 views • link
written by GenoMax GenoMax

1 answer

You need to download the linux-64 version of conda, not the 32bit version.

• 0 views • link
written by Devon Ryan Devon Ryan

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