Closed AndrewLangvt closed 6 years ago
Hi @AndrewLangvt, Did you run the executable with -h
flag to see the available options?
One of them --index
is indeed to specify the output prefix of the graph you are building.. I would suggest using it to specify a directory/prefix that you have writable access to (it seems you do not have permission to write to Whippet.jl/index/
). By default it outputs to Whippet.jl/index/graph
and adds the .jls
. So you will want to exclude the .jls
from what you supply to this option, e.g. --index some/path/you/have/access/to/graph_name_or_genome_build
I will try to think of how best to improve the documentation for these sorts of situations.
Thanks for the quick reply @timbitz. I feel rather silly now. I did not run with the -h
flag; I was just following through the walk-through directions here on GitHub. I'll be sure to dig into each command more thoroughly in the future, recognizing that the documentation may not have all of the flags laid out within. I appreciate the help, specifying the index location did the trick!
Hi @AndrewLangvt, Yah my apologies for that. The walk-through directions were meant to be simple and illustrate Whippet's ease-of-use with default parameters, which should be suitable for the vast majority of users. However, that inadvertently made it less intuitive to use for those who require the non-default parameters, which have not all been sufficiently documented perhaps.
I have added a tad bit of rough documentation (to master) in the walk-through directions for non-default names & locations of whippet indexes and to point users to the command line flags. However perhaps this is still lacking a tad, and I should really add a separate section that goes into more detail on each parameter. I will think about the best way to do this while still maintaining the base simplicity of the docs.
Hey @timbitz,
Currently, whippet is installed on a shared directory in our computing cluster and I am thinking this may be where my issue is stemming from. Whipped will parse through the GTF, build splice graphs, and then error out when attempting to open graphs.jls. There is no such file that I can see at the location specified. Is this a graph file whippet is attempting to build? And if so, I am guessing it is run-specific, such that having it installed in a central directory may be where the permissions error is arising from?