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Andrey ARISTOV
multichip-snakemake
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8b38f28b
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8b38f28b
authored
3 years ago
by
Andrey ARISTOV
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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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