Commit bfab2219 authored by Sam Nooij's avatar Sam Nooij
Browse files

Add download instruction

parent 576359c1
......@@ -74,9 +74,32 @@ This project uses Python 3 and PyYAML. These may be installed with [`conda`](htt
## User manual
### 1. Preparing data
### 1. Download the pipeline
#### Importing from Jovian
To download the pipeline from this page, use git clone:
```bash
git clone git@git.lumc.nl:snooij/jovian-screener.git
```
(Also see the 'Clone' button at the top of this page for the SSH and HTTPS links.)
Then, optionally change the name of the newly downloaded directory:
```bash
mv jovian-screener My_new_project
```
And change directory into this new project to get started:
```bash
cd My_new_project
```
_(N.B. Change 'My_new_project' to whatever name you like for your directory!)_
### 2. Prepare data
#### Import from Jovian
This project includes a Python script that can import all required output files from Jovian into the desired new project directory.
_This is the recommended way of importing data._
......@@ -85,22 +108,28 @@ To use it, one needs to have run Jovian and preferably have created a new direct
Also, the script requires PyYAML to be installed.
If you did this with conda, activate the corresponding conda environment before running the next commands, e.g.:
`conda activate pyyaml`
```bash
conda activate pyyaml
```
If you are currently in this new directory, which sits next to the Jovian directory, called `Jovian`, the importer script can be used as follows:
`bin/import_jovian_output.py -i ../Jovian/ -o ./`
```bash
bin/import_jovian_output.py -i ../Jovian/ -o ./
```
(Where `-i` stands for input, `../Jovian/` points to Jovian's main directory or folder,
`-o` stands for output, and `./` is the current working directory.)
By default, the script will move the files from Jovian's directory. If you want to make a new copy, instead use:
`bin/import_jovian_output.py -i ../Jovian/ -o ./ -m copy`
```bash
bin/import_jovian_output.py -i ../Jovian/ -o ./ -m copy
```
(Where `-m` can be used to select the mode: copy, move or link.)
#### Choosing a reference
#### Choose a reference
The data to be screened is now ready. Next up is the sequence and/or species to be screened for.
This sequence should be saved (in fasta format) and the file path should be added to the configuration file `config/config.yaml` in the line that starts with `reference: `.
......
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