Question: conda tophat installation error
0
gravatar for amitunited0532
18 months ago by
amitunited053210 wrote:
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.

anaconda python • 1.7k views
ADD COMMENTlink modified 18 months ago by finswimmer13k • written 18 months ago by amitunited053210
1

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.

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax77k

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.
ADD REPLYlink modified 18 months ago by finswimmer13k • written 18 months ago by amitunited053210

Go for a faster aligner like Hisat2, Star etc.

ADD REPLYlink written 18 months ago by arup1.9k

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

ADD REPLYlink written 18 months ago by amitunited053210
1

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?

ADD REPLYlink written 18 months ago by genomax77k

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

ADD REPLYlink written 18 months ago by Devon Ryan93k
0
gravatar for Devon Ryan
18 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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

ADD COMMENTlink written 18 months ago by Devon Ryan93k
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