Merge pull request #291 from bbglab/dev-qmap-newCPD

Revise Qmap submission instructions in the new Data Center

Author: migrau

docs/Cluster_basics/Submitting_jobs/Qmap.md

@@ -1,3 +1,4 @@
+
 # Qmap Submit
 
 ## Description
@@ -10,43 +11,95 @@ How to submit jobs to the Cluster using **Qmap**.
 
 ### 1. Prepare .qmap file (example)
 
-```bash
-[params]
-memory=50G
+=== "IRB cluster"
+
+    ```bash 
+    [params]
+    memory=50G
+
+    [pre]
+    ml load anaconda3  #OR . "/home/$USER/miniconda3/etc/profile.d/conda.sh"
+    conda activate sciclone-env
+
+    [jobs]
+    Rscript run.R ../data/vafs.dat bmm 3 ./results.beta.3
+    Rscript run.R ../data/vafs.dat gaussian.bmm 3 ./results.gaussian.3
+    Rscript run.R ../data/vafs.dat binomial.bmm 3 ./results.binomial.3
+    ```
+
+=== "BBG cluster"
+
+    ```bash
+    [params]
+    memory=50G
+
+    [pre]
+    . "/home/$USER/miniconda3/etc/profile.d/conda.sh"
+    conda activate sciclone-env
+
+    [jobs]
+    Rscript run.R ../data/vafs.dat bmm 3 ./results.beta.3
+    Rscript run.R ../data/vafs.dat gaussian.bmm 3 ./results.gaussian.3
+    Rscript run.R ../data/vafs.dat binomial.bmm 3 ./results.binomial.3
+    ```
+
+The only difference is how you load conda. On the IRB cluster, you can use either of the following options:
 
-[pre]
- . "/home/$USER/miniconda3/etc/profile.d/conda.sh"
-conda activate sciclone-env
+ 1) Use the pre-installed conda module (`ml load anaconda3`)
 
-[jobs]
-Rscript run.R ../data/vafs.dat bmm 3 ./results.beta.3
-Rscript run.R ../data/vafs.dat gaussian.bmm 3 ./results.gaussian.3
-Rscript run.R ../data/vafs.dat binomial.bmm 3 ./results.binomial.3
+ 2) If you use mamba or prefer to use your own conda installation,
+  load it the same way you do on the BBG cluster:
 
-```
+  `. "/home/$USER/miniforge3/etc/profile.d/conda.sh"`
+
+   For micromamba:
+
+  `eval "$(micromamba shell hook --shell=bash)"`
 
 ### 2. Run "qmap submit" from the login node
 
-```bash
-qmap submit filename.qmap
+=== "IRB cluster"
+
+    ```bash 
+    interactive
+    spack load py-qmap
+    qmap submit filename.qmap
+    ```
 
-```
+=== "BBG cluster"
 
-## Aditional info
+    ```bash
+    qmap submit filename.qmap
+    ```
+
+## Additional info
 
 ### Extra parameters
 
 If you need to provide any [extra parameter](https://qmap.readthedocs.io/en/latest/concepts.html#parameters) directly to
 SLURM, you can do it defining a new profile.config file. E.g.
 
-```toml
-executor = slurm
+=== "IRB cluster"
+
+    ```bash
+    executor = slurm
+
+    [params]
+    extra = -G 1
+    ```
+
+=== "BBG cluster"
+
+    ```bash
+    executor = slurm
+
+    [params]
+    extra = -p bigmem
+    ```
 
-[params]
-extra = -p bigmem
-```
+By default, the queue used in the BBG cluster is `bigrun`.
 
-By default, the queue used is `bigrun`.
+For Qmap runs using GPUs, use `-G 1`.
 
 ## Reference