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Commit 8c8829dd authored by julie.orjuela_ird.fr's avatar julie.orjuela_ird.fr
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minors doc installation part into README

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......@@ -71,7 +71,7 @@ In local mode, it's possible to allocate threads to some rules using `--set-thre
### 2.2 Running your data in CLUSTER mode
Now you can launch suggested command line done by RNAja in `cluster` mode BUT before you need to configurate cluster parameters running command line 'RNAja edit_cluster_config' before the first run and modify threads, ram, node and computer resources.
Now you can launch suggested command line done by RNAja in `cluster` mode BUT before you need to configurate cluster parameters running command line `RNAja edit_cluster_config` before the first run and modify threads, ram, node and computer resources.
RNAja does a copy of `cluster_config.yaml` file into your home `"/home/$USER/.config/rnaja_pipeline/cluster_config.yaml"`
```bash
......@@ -86,13 +86,13 @@ If singularity was selected in installation of RNAja, it could be needed to give
RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind $HOME"
# here a example adapted to @IFB HPC
#RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind /shared:/shared"
RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind /shared:/shared"
#you can also use snakemake parameters as
#RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind $HOME" --rerun-incomplete --nolock
RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind $HOME" --rerun-incomplete --nolock
```
**Important Note** : In i-Trop cluster, run RNAja using ONLY a node, data has to be in "/scratch" of chosen node. Use `nodelist : nodeX` parameter inside of `cluster_config.yaml`̀ file.
**Important Note** : In IRD "i-Trop" cluster, run RNAja using ONLY a node, data has to be in "/scratch" of chosen node. Use `nodelist : nodeX` parameter inside of `cluster_config.yaml`̀ file.
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### Authors
......@@ -107,7 +107,7 @@ Some parts of RNAja code and documentation were inspired or came from the pipeli
- BulkRNA (Camille Cohen) https://github.com/CamilleCohen/ProjetTuteur-_BulkRNA
RNAja uses SnakEcdysis package https://snakecdysis.readthedocs.io/en/latest/package.html to perform installation and execution in local and cluster mode developed by Sébastien Ravel (CIRAD).
RNAja uses really nice python package **SnakEcdysis** https://snakecdysis.readthedocs.io/en/latest/package.html to perform installation and execution in local and cluster mode. SnakEcdysis is developed by Sébastien Ravel (CIRAD).
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## Acknowledgements
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