The install README does not list BLAZE as an (optional) dependency.
More generally, the docs simply state:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("FLAMES")
...but there are other system-level dependencies that will not be installed via the BiocManager. From the DESCRIPTION:
SystemRequirements: GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17)
It would be helpful to list all system-level dependencies in the README install instructions, and how to install these system-level dependencies.
For example:
mamba create -n flames \
python=3.10 "samtools>=1.14" "minimap2>=2.28" pysam numpy editdistance \
blaze2 bioconductor-flames
... along with pip3 install blaze2, since there is no conda recipe for blaze. Given the lack of the recipe, one could use:
channels:
- conda-forge
- bioconda
dependencies:
- python=3.10
- numpy
- pysam
- editdistance
- samtools>=1.14
- minimap2>=2.28
- bioconductor-flames
- pip
- pip:
- blaze2It would be helpful to know which versions of numpy, pysam and editdistance are supported.
I should note that installing flames via conda is MUCH faster than compiling all the C code for all R packages when using BiocManager::install("FLAMES").
The install README does not list BLAZE as an (optional) dependency.
More generally, the docs simply state:
...but there are other system-level dependencies that will not be installed via the BiocManager. From the DESCRIPTION:
It would be helpful to list all system-level dependencies in the README install instructions, and how to install these system-level dependencies.
For example:
... along with
pip3 install blaze2, since there is no conda recipe for blaze. Given the lack of the recipe, one could use:It would be helpful to know which versions of
numpy,pysamandeditdistanceare supported.I should note that installing flames via conda is MUCH faster than compiling all the C code for all R packages when using
BiocManager::install("FLAMES").