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Commit 8b38f28b authored by Andrey  ARISTOV's avatar Andrey ARISTOV
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Update README.md

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...@@ -6,6 +6,14 @@ This a snakemake pipeline allowing to reconstruct the 6-chips data automatically ...@@ -6,6 +6,14 @@ This a snakemake pipeline allowing to reconstruct the 6-chips data automatically
## Running locally ## Running locally
On Elissa computer find and launch the icon on the desktop "Snakemake".
The terminal will open.
The command to launch reconstruction:
```
snakemake -c12 D:\Andrey\Data\path_to_final_table.csv
```
For conveniense it is possible to drag and drop the folder into the terminal to get a valid path, then simply add the missing filename at the end.
## Running on the cluster ## Running on the cluster
``` ```
...@@ -13,5 +21,7 @@ ssh USERNAME@maestro.pasteur.fr ...@@ -13,5 +21,7 @@ ssh USERNAME@maestro.pasteur.fr
snk snk
snakemake --cluster "srun -c12" -j32 ~/Anchor/Lena/Data/20220531-MIC-e.coli-cipro/{1st,2nd}exp/final_table.csv --cores 12 snakemake --cluster "srun -c12" -j32 ~/Anchor/Lena/Data/20220531-MIC-e.coli-cipro/{1st,2nd}exp/final_table.csv --cores 12
``` ```
In another terminal you can see the status of the jobs using sacct In another terminal you can see the status of the jobs using *sacct*
``` watch sacct``` ```
watch sacct
```
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