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 ...@@ -74,9 +74,32 @@ This project uses Python 3 and PyYAML. These may be installed with [`conda`](htt
## User manual ## 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 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._ _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 ...@@ -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. 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.: 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: 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, (Where `-i` stands for input, `../Jovian/` points to Jovian's main directory or folder,
`-o` stands for output, and `./` is the current working directory.) `-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: 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.) (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. 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: `. 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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