tophat2 installation error

Question

[Adyasha]

Hi,

I am trying to install tophat2 .

tried this command

conda install -c bioinfo tophat2

but got this error :

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
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:

  - tophat2

Current channels:

  - https://conda.anaconda.org/bioinfo/linux-64
  - https://conda.anaconda.org/bioinfo/noarch
  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - 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


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.

Anyone know how can I install tophat2 and run it if I get this error .

when I try this command

conda install -c bioconda tophat

I get this error

install -c bioconda tophat

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.                                                                                                                                                         failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - tophat -> python[version='2.7.*|>=2.7,<2.8.0a0|<3']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0

Your installed version is: 2.17

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

Please help Thanks

Answer 1

[Carlo Yague]

Please note that Tophat2 is deprecated. Unless you have a good reason to use Tophat2, more recent aligners such as STAR or HISAT2 should be used instead.

Now to solve your problem, creating a new environment should do the trick.

conda create -n tophat_env
conda activate tophat_env
conda install -c bioconda tophat

[Adyasha]

Hi sir,

I have tried using hisat2 also,

hisat2 -x BOWTIE_INDEX/ -1 A_R1.val.fq -2 A_R2.val.fq -S out.sam

but its saying :

(ERR): "BOWTIE_INDEX/" does not exist

I have

bowtie_index.1.bt2

bowtie_index.2.bt2

bowtie_index.3.bt2

bowtie_index.4.bt2

bowtie_index.rev.1.bt2

bowtie_index.rev.2.bt

theses files in my BOWTIE_INDEX folder.

[Carlo Yague]

Assuming the BOWTIE_INDEX folder is in your current directory, then you should write hisat2 -x BOWTIE_INDEX/bowtie_index (-x goes with the PATH and basename of the index)