Commit 29195043 authored by VIENNE MAINA's avatar VIENNE MAINA
Browse files

update docs + add environement variables

parent 6b4dd74d
......@@ -5,18 +5,17 @@
1. Install metagwgs as described here: [installation doc](../docs/installation.md)
2. Get datasets: two datasets are currently available for these functional tests at `https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git`
Replace "\<dataset\>" with either "small" or "mag":
```
git clone --branch <dataset> git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git
git clone git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git
or
wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/archive/<dataset>/metagwgs-test-datasets-<dataset>.tar.gz
wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git
```
3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz ) and decompress its contents in any folder. This archive contains data banks for:
3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz) and decompress its contents in any folder. This archive contains data banks for:
- **Kaiju** (_kaijudb_refseq_2020-05-25_)
- **Diamond** (_refseq_bacteria_2021-05-20_)
- **NCBI Taxonomy** (_taxonomy_2021-08-23_)
- **NCBI Taxonomy** (_taxonomy_2021-12-7_ )
- **Eggnog Mapper** (_eggnog-mapper-2.0.4-rf1_)
......@@ -30,15 +29,34 @@ To launch functional tests, you need to be located at the root of the folder whe
- by providing the results folder of a pipeline already exectuted
```
cd test_folder
python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results
export METAG_PATH="/path/to/sources"
export DATASET="/path/to/metagwgs-test-datasets"
python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results
```
- by providing a script which will launch the nextflow pipeline [see example](./launch_example.sh) (this example is designed for the "small" dataset with --min_contigs_cpm>1000, using slurm)
```
mkdir test_folder
cd test_folder
cp <metagwgs-src>/functional_tests/launch_example.sh ./
python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results --script launch_example.sh
```
1. create working directory
```
mkdir test_folder
cd test_folder
```
2.set enviroment variables and load module
```
export METAG_PATH="/path/to/sources"
export DATASET="/path/to/metagwgs-test-datasets"
export DATABANK="/path/to/FT_banks_2021-10-19"
export EGGNOG_DB="$DATABANK/eggnog-mapper-2.0.4-rf1/data"
module load system/Python-3.7.4
```
3.launch functional test
```
cp $METAG_PATH/functional_tests/launch_example.sh ./
python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results --script launch_example.sh
```
>**NOTE: more information on the command used to produce each dataset in [small](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/small) and [mag](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/mag) READMEs**
......
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