Differences

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--- sagsub [2024/02/27 10:03] – Luc Bonnefond
+++ sagsub [2024/08/29 06:56] (current) – Luc Bonnefond
@@ Line 2: / Line 2: @@
 Requested files :
-  * GridTools.py
+  * {{ :gridtools.py |}}
-  * MRC_RW_3.py
+  * {{ :mrc_rw_3.py |}}
-  * Pattern_Optimizer.py
+  * {{ :pattern_optimizer.py |}}
-  * SAGsub_3-2_stable_parallel_Nils.py
+  * {{ :sagsub_3-2_stable_parallel_nils.py |}}
-Place them all in a SAGsub3 folder in your home directory (<quote>~/SAGsub3/</quote>)
+Log onto the Lamour GPU node:
+<code>
+ssh my_login@hpc.igbmc.fr
+ssh my_login@phantom-node39
+</code>
-Most of the required python libraries are already available on the python hpc. Only the mrcfile library is missing and should be installed on phantom-node39 (I already did it, but I am not sure if its available for other account then mine)
+Place the 4 python scripts in a SAGsub3 folder in your hpc home directory (<quote>~/SAGsub3/</quote>)
+Most of the required python libraries are already available on the python module available on the igbmc hpc. Only the mrcfile library is missing and should be installed on phantom-node39 (I already did it, but I am not sure if its available for other account then mine)
 <code>
-ssh login@hpc.igbmc.fr
+ssh my_login@hpc.igbmc.fr
-ssh login@phantom-node39
+ssh my_login@phantom-node39
 module load python/3.9
 pip3 install mrcfile
 </code>
-Go to the folder containing the motion corrected micrographs to which the lattice subtraction needs to be applied (it can be resumed if it was partially ran before). Rub the command:
+Go to the folder containing the motion corrected micrographs to which the lattice subtraction needs to be applied (it can be resumed if it was partially ran before).
+From the igbmc hpc, the storage path is : <quote>/shared/misc/cbi-teams/</quote>
+Run the command:
 <code>
-python3 ~/SAGsub3/SAGsub_3-2_stable_parallel_Nils.py --force_apix 0.729
+python3 ~/SAGsub3/sagsub_3-2_stable_parallel_nils.py --force_apix 0.729
 </code>
-The <quote>--force_apix 0.729</quote> is for Krios2 datasets; it needs to be changed for the other microscopes/cameras
+The <quote>--force_apix 0.729</quote> is for Krios2 datasets; it needs to be changed for the other microscopes/cameras (0.862 for Krios1 and 0.901 for Glacios)
 Useful commands:
@@ Line 29: / Line 39: @@
   * <quote>fg</quote> to bring the job to the foreground
-You can check the results in the <quote>SAGsub.star</quote> file
+You can check the results in the <quote>SAGsub.star</quote> file, formatted with different columns:
-Format, with different columns:
   - Micrograph name
   - Mosaicity (should be 1 most of the time)