There are no available installation conda packages

[hongman2006]

Solving environment: failed

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

• lifton

Current channels:

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

To search for alternate channels that may provide the conda package you're
looking for, navigate to

[Kuanhao-Chao]

Hi @hongman2006,

LiftOn is not on bioconda yet. We are working on it. You can first try to install it through pip.
Please check this page: https://ccb.jhu.edu/lifton/content/installation.html
Please let me know if you have further question about the installation

[TDDB-limagrain]

Hi @Kuanhao-Chao,
it seems that the installation also needs pytest.
In addition, in the requirements, you should replace parasail by parasail-python.

Congrats for the tool otherwise!

[Kuanhao-Chao]

Hi @TDDB-limagrain,
Thanks for reporting this issue. I have added pytest to the setup.py dependencies, as the Liftoff test scripts depend on it. If you are not running the test scripts, the pytest dependency can be ignored. I have also checked the parasail package and believe it is the correct requirement: https://github.com/jeffdaily/parasail-python

Let me know if you encounter any problems installing LiftOn

[TDDB-limagrain]

Ok this was because I added parasail by conda, not by pip.
Below it the yml file I created for a capsule conda environment:

name: envLiftOn
channels:
    - conda-forge
    - default
    - bioconda
dependencies:
    - python>=3.8.0
    - numpy>=1.22.0
    - gffutils>=0.10.1
    - biopython>=1.76
    - cigar>=0.1.3
    - parasail-python>=1.2.4
    - intervaltree>=3.1.0
    - networkx>=2.4
    - interlap>=0.2.6
    - pyfaidx>=0.5.8
    - pysam>=0.19.1
    - ujson>=3.2.0

then I used the pip within that environment to install lifton.

[Kuanhao-Chao]

@TDDB-limagrain Thanks for reporting this. We are working on the conda package and will resolve this problem. For now, you can try uninstalling parasail-pythonand installingparasail through pip.