This page is just meant for general questions that I notice are asked with some frequency. If you feel like something is missing from here and you'd like to see it included, feel free to ask it by raising an issue on GitHub.
A known issue with using snakemake + pysam + qsub results in the a break in the pipeline. The issue arises because pysam
does not activate correctly when using qsub by default. To fix this you just need to add the -V
parameter to your qsub
command.
It is probably best to just let Aviary handle the downloading of your databases via the --download
parameter. But, if you
would like to set them up yourself, please read ahead
For the GTDB:
db/
folder inside of that download.The optional databases are as follows:
Aviary will ask for the paths to these database files if they don't exist, otherwise you can place these lines into
the activate.d/aviary.sh
or .bashrc
files changing the specific paths:
export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release207/db/ # https://gtdb.ecogenomic.org/downloads
export EGGNOG_DATA_DIR=/path/to/eggnog-mapper/2.1.7/ # https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.7#setup
export CONDA_ENV_PATH=/path/to/conda/envs/
Put all your birds in one place.
I made it (among other bird based + CoverM logos) using GIMP and based the idea off of this tutorial. They are very easy to make so just follow that video if you feel like making something similar.
You sound like my supervisor.
Powered by Doctave