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seqan
Flexbar package not found in Bioconda
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.
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
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
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']
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
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!