samtools dependency

It might be worthwhile to add samtools to the installation requirements list. I used the suggested command:

conda install numpy scipy cython numba matplotlib scikit-learn h5py click

Then I found out about the samtools requirement after trying to run velocyto. Installing samtools separately led to numpy version conflicts. It was fixable, but it’s probably best to just add it to the initial install command.

On a related note, pandas is also a requirement, but it is not listed.

[slinnarsson]

Ok, I never noticed probably because I had samtools installed for some other reason. If the code is not too complicated and you want to drop the dependency on samtools instead, you can run any samtools command from pysam:

pysam.sort("-o", "output.bam", "ex1.bam")

[sky1ove]

for linux/ ubuntu, I solved this problem by ‘sudo apt-install samtools’