Louis BECQUEY / RNANet

Go to a project
Toggle navigation Toggle navigation pinning
Louis BECQUEY
d8eb4c71 1 parent 1854316d

automation script for EvryRNA

Inline Side-by-side
Showing 2 changed files with 11 additions and 3 deletions
...@@ -1411,7 +1411,10 @@ class Pipeline: ...@@ -1411,7 +1411,10 @@ class Pipeline:
1411 subprocess.run(["tar","-C", path_to_3D_data + "/datapoints","-czf",f"results/archive/RNANET_datapoints_{time_str}.tar.gz","."]) 1411 subprocess.run(["tar","-C", path_to_3D_data + "/datapoints","-czf",f"results/archive/RNANET_datapoints_{time_str}.tar.gz","."])
1412 1412
1413 # Update shortcuts to latest versions 1413 # Update shortcuts to latest versions
1414 - subprocess.run(["rm", "-f", runDir + "/results/RNANET_datapoints_latest.tar.gz", runDir + "/results/summary_latest.csv", runDir + "/results/families_latest.csv"]) 1414 + subprocess.run(["rm", "-f", runDir + "/results/RNANET_datapoints_latest.tar.gz",
1415 + runDir + "/results/summary_latest.csv",
1416 + runDir + "/results/families_latest.csv"
1417 + ])
1415 subprocess.run(['ln',"-s", runDir +f"/results/archive/RNANET_datapoints_{time_str}.tar.gz", runDir + "/results/RNANET_datapoints_latest.tar.gz"]) 1418 subprocess.run(['ln',"-s", runDir +f"/results/archive/RNANET_datapoints_{time_str}.tar.gz", runDir + "/results/RNANET_datapoints_latest.tar.gz"])
1416 subprocess.run(['ln',"-s", runDir +f"/results/archive/summary_{time_str}.csv", runDir + "/results/summary_latest.csv"]) 1419 subprocess.run(['ln',"-s", runDir +f"/results/archive/summary_{time_str}.csv", runDir + "/results/summary_latest.csv"])
1417 subprocess.run(['ln',"-s", runDir +f"/results/archive/families_{time_str}.csv", runDir + "/results/families_latest.csv"]) 1420 subprocess.run(['ln',"-s", runDir +f"/results/archive/families_{time_str}.csv", runDir + "/results/families_latest.csv"])
......
1 # This is a script supposed to be run periodically as a cron job 1 # This is a script supposed to be run periodically as a cron job
2 2
3 -# Run RNANet
4 cd /home/lbecquey/Projects/RNANet; 3 cd /home/lbecquey/Projects/RNANet;
5 rm -f stdout.txt stderr.txt errors.txt; 4 rm -f stdout.txt stderr.txt errors.txt;
5 +
6 +# Run RNANet
6 time './RNAnet.py --3d-folder /home/lbequey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -s -r 20.0 --archive' > stdout.txt 2> stderr.txt; 7 time './RNAnet.py --3d-folder /home/lbequey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -s -r 20.0 --archive' > stdout.txt 2> stderr.txt;
7 8
9 +# Compress
10 +rm -f results/RNANet.db.gz
11 +gzip -k results/RNANet.db
12 +
8 # Sync in Seafile 13 # Sync in Seafile
9 seaf-cli start; 14 seaf-cli start;
10 - 15 +sleep 1h;
11 seaf-cli stop; 16 seaf-cli stop;
12 17
......