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
.
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?