vanheeringen-lab/genomepy

instead of throwing gtfToGenePred errors it should tell user that they should be installed, otherwise users will think annotation download is broken

antonkulaga opened this issue · 2 comments

antonkulaga commented

Whenever I try to download Ensembl genomes for human and mice I get:

/bin/sh: 1: gtfToGenePred: not found

For half and hour I thought that Ensembl support is broken. I believe the error message should explicitly say I should install some console tools. Or, actually it can allow downloading everything but gene-pred stuff, because it is often enough to just download gtf and process it yourself

simonvh commented

Hi @antonkulaga, can I ask how you installed genomepy? When you install genomepy via conda, then gtfToGenePred should be installed as a dependency. If you installed it via pip, then indeed you need to install some UCSC tools (as is described in the installation guide). I do agree that the message can be more informative when a required dependency is not found.

siebrenf commented

A more descriptive error will be raised with genomepy 0.15!