Collection of scripts and tricks that help automate collecting / formatting / checking the data from the obervatories
List of tools (in /pyedm)
| code | name | purpose |
|---|---|---|
| gg | google-get | gets csv content from the managed google-documents |
| ena | ena | creates / updates / gets info from objects in the ENA database |
These tools have not been published yet so using them requires a local git checkout of the source, a virtualenv to work in, and then a straightforward install into that.
On windows we recommend having gitbash around to execute this. Gitbash is part of git-scm
- open a bash terminal
- double check if you have python there:
$ python --version- get the source code for the project - and enter the project
$ git clone [email protected]:emo-bon/emobon-dm-tools.git
$ cd emobon-dm-tools- create a virtualenv and activate it
$ virtualenv venv -p python3
$ source ./${venv}/bin/activate- install the tools and check
$ make init-dev
$ python -m pydem --helpUsage of specific tools is explained in detail below
python -m pyedm.gg -g ../observatory-BPNS
pythin -m pyedm.ena -s ../sequencing-data/shipment/2022-07-14_samples.csv