Comments (5)
@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.
from lifton.
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
from lifton.
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!
from lifton.
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
from 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
.
from lifton.
Related Issues (20)
- FeatureNotFoundError with gffutils HOT 3
- gffutils error at stage "Populating features" HOT 2
- Weird formatting of column 9 in gff3 lift-over
- parasail_memalign: posix_memalign failed: Cannot allocate memory
- accept gtf format
- lifton installation error [pip]
- gffutils database build failed with UNIQUE constraint failed: features.id
- race conditions HOT 3
- Develop a version suitable for bacteria? HOT 1
- Provided CHM13 file has incorrect exons
- can not find the installed miniprot HOT 1
- can not creating DNA dictionary/protein dictionary from the reference annotation and error in miniprot
- Installation with pip fails, requiring networkx>=3.3
- Inquiry on Resolving Long Chromosome Sequences in Analysis
- Python errors when running lifton HOT 2
- LiftOn silently failing due to ID feature
- Reference annotation database construction get's stuck
- LiftOff generates better BUSCO scores than LiftOn HOT 2
- gffutils database build failed with No lines parsed HOT 1
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