Flexbar package not found in Bioconda

[TeodoraTockovska]

Hi! I am trying to install Flexbar using Miniconda, but the package isn't found in any channels. I searched for Flexbar in the bioconda channels using the following command: conda search flexbar

Below are the printed messages after running the command above:

Loading channels: done
No match found for: flexbar. Search: flexbar

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

• flexbar

Current channels:

• https://repo.anaconda.com/pkgs/main/osx-arm64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/osx-arm64
• 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.

[tony-travis]

Hi,
It's because an arm64 version is not available in the osx channels you're searching. It is available in the x86_64 Linux channels:

conda search flexbar
Loading channels: done
# Name                       Version           Build  Channel             
flexbar                        2.5.0               0  bioconda            
flexbar                        2.5.0               1  bioconda            
flexbar                        2.5.0      h21aa3a5_2  bioconda            
flexbar                        2.5.0      h2823f96_4  bioconda            
flexbar                        2.5.0      hb7ba0dd_3  bioconda            
flexbar                        2.5.0      hf53871c_5  bioconda            
flexbar                        3.3.0               1  bioconda            
flexbar                        3.5.0      h2823f96_4  bioconda            
flexbar                        3.5.0      hb7ba0dd_3  bioconda            
flexbar                        3.5.0      hf3e9acd_2  bioconda            
flexbar                        3.5.0      hf53871c_5  bioconda            
flexbar                        3.5.0      hf53871c_6  bioconda            

lsb_release -d
Description:	Ubuntu 22.04.1 LTS
inxi
CPU: 2x 8-core AMD Opteron 6276 (-MT MCP MCM SMP-)
speed/min/max: 1462/1400/2300 MHz Kernel: 5.15.0-57-generic x86_64
Up: 7d 23h 14m Mem: 70021.7/257921.7 MiB (27.1%)
Storage: 42.49 TiB (31.0% used) Procs: 1180 Shell: Bash inxi: 3.3.13

[tony-travis]

These are the channels in my conda config:

           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/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
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch

[TeodoraTockovska]

Thank you for the fast response, I appreciate it! I tried to install flexbar using the channel that contained the package but I ran into a new error where it seems there are incompatibility issues.

conda install --channel https://conda.anaconda.org/bioconda/linux-64 flexbar

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.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package bzip2 conflicts for:
python=3.10 -> bzip2[version='>=1.0.8,<2.0a0']
flexbar -> bzip2[version='1.0.*|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']

[tony-travis]

The problem is in your env:

(base) user@host:~$ conda create -n flexbar
Collecting package metadata (current_repodata.json): done
Solving environment: done
[...]
Proceed ([y]/n)? 

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate flexbar
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) user@host:~$ conda activate flexbar
(flexbar) user@host:~$ conda install flexbar
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/user/.conda/envs/flexbar

  added / updated specs:
    - flexbar


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    flexbar-3.5.0              |       hf53871c_6         384 KB  bioconda
    libgcc-ng-12.2.0           |      h65d4601_19         931 KB  conda-forge
    libgomp-12.2.0             |      h65d4601_19         455 KB  conda-forge
    libstdcxx-ng-12.2.0        |      h46fd767_19         4.3 MB  conda-forge
    libzlib-1.2.13             |       h166bdaf_4          64 KB  conda-forge
    seqan-library-2.4.0        |                0         6.1 MB  conda-forge
    tbb-2020.2                 |       h4bd325d_4         1.5 MB  conda-forge
    zlib-1.2.13                |       h166bdaf_4          92 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        13.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  flexbar            bioconda/linux-64::flexbar-3.5.0-hf53871c_6
  libgcc-ng          conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
  libgomp            conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19
  libzlib            conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
  seqan-library      conda-forge/linux-64::seqan-library-2.4.0-0
  tbb                conda-forge/linux-64::tbb-2020.2-h4bd325d_4
  zlib               conda-forge/linux-64::zlib-1.2.13-h166bdaf_4


Proceed ([y]/n)? 


Downloading and Extracting Packages
libstdcxx-ng-12.2.0  | 4.3 MB    | ######################################################################################### | 100% 
tbb-2020.2           | 1.5 MB    | ######################################################################################### | 100% 
zlib-1.2.13          | 92 KB     | ######################################################################################### | 100% 
libgcc-ng-12.2.0     | 931 KB    | ######################################################################################### | 100% 
libzlib-1.2.13       | 64 KB     | ######################################################################################### | 100% 
seqan-library-2.4.0  | 6.1 MB    | ######################################################################################### | 100% 
flexbar-3.5.0        | 384 KB    | ######################################################################################### | 100% 
libgomp-12.2.0       | 455 KB    | ######################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(flexbar)user@host:~$ 
(flexbar) user@host~$ flexbar --version

flexbar version: 3.5.0
SeqAn version: 2.4.0
(flexbar) user@host:~$ python3 -V
Python 3.10.6

[TeodoraTockovska]

The installation failed again. I am uncertain what happened as i was able to create the environment without issues. I do appreciate your assistance, thank you!