Comments (5)
tony-travis
commented on August 25, 2024
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
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tony-travis
commented on August 25, 2024
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
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TeodoraTockovska
commented on August 25, 2024
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.
failedUnsatisfiableError: 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']
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tony-travis
commented on August 25, 2024
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
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TeodoraTockovska
commented on August 25, 2024
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!
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Related Issues (20)
- NextFlex UMI detection HOT 1
- combining adapters and barcode removal into a single command paired-end fastq
- paired end barcode demultiplexing HOT 1
- -ap ONLY mode does not use -at RIGHT vs -at LEFT
- error when building from source: CMake Error: The source directory "/flexbar-3.5.0" does not appear to contain CMakeLists.txt. HOT 3
- Issue downloading flexbar from source HOT 2
- error while installing from source 3.50 version HOT 1
- conda install flexbar error
- Flexbar could't identify Y base?
- Flexbar will not produce output file
- Demultiplexed a single read with barcodes at both ends
- Not able to run flexbar with paired reads
- UMI tags can't be add to reads name properly while pair end mode
- Please upgrade to onetbb HOT 7
- Unexpected end of input. HOT 4
- Supporting Flexbar in easybuild
- Exclude some barcodes combinations ?
- flexbar: Too many arguments! HOT 2
- Question about setting parameters
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