Open hongman2006 opened 4 months ago
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
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!
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
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
.
@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.
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to