`pip install kneaddata` doesn't install dependencies

Infrastructure and utilities KneadData
1

When using pip dependencies such as trimmomatic or bowtie2 aren’t installed.
The docker biobakery/Dockerfile at master · biobakery/biobakery · GitHub will not run kneaddata, as it fails to find trimmomatic and bowtie2 in $PATH .

2

Yes, even the conda recipe doesn’t install dependencies like BMTagger or TRF or srprism and BMtools. I am having a hard time using making hg48 indexes because of the inability to compile Srprism on HPC. Can these dependencies be included in conda package?

3

@sagunmaharjann

The pip install kneaddata did not install the dependencies (Trimmomatic, bowtie2, trf)

Is it due to any error or should we download/install the dependencies separately?

Thanks,
Shrez