conda tophat installation error

Question

[amitunited0532]

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.

[GenoMax]

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.

[amitunited0532]

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.

[Arup Ghosh]

Go for a faster aligner like Hisat2, Star etc.

[amitunited0532]

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

[GenoMax]

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?

[Devon Ryan]

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

Answer 1

[Devon Ryan]

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