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ctg-lund / singleCellWorkflows

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Specify to which person a delivery script will send the email to. #38

Closed Fattigman closed 1 year ago

Fattigman commented 1 year ago

Problem

The email script today is hardcoded to be delivered to myself. This is suboptimal if someone else at CTG want to run the pipeline, it will still be delivered to me.

Suggestion

Add a config parameter that is tells the script which person the data is going to get delivered to.

Can be closed when:

Note

This is still a temporary solution, as the final solution will be a delivery routine by Yggdrasil or another delivery method.

chaetognatha commented 1 year ago

Didn't we get an email that points to the whole bioinformatics team?

Fattigman commented 1 year ago

When has it ever done that?

chaetognatha commented 1 year ago

Because an alias that points to all of us would be a great default

chaetognatha commented 1 year ago

So I edited the delivery script that is under Yggdrasil/bin/delivery.sh This is how it works now:

-rw-rw-r-- 1 mattis ls-grupp4 30 Aug 24 14:00 10.txt

mattis@ls4-fe1 /projects/fs1/shared/Test_Jobs/Tiny_Test $
cat *
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023
Thu Aug 24 14:00:59 CEST 2023

mattis@ls4-fe1 /projects/fs1/shared/Test_Jobs/Tiny_Test $
bash ~/Shared/Yggdrasil/bin/delivery.sh 
Error: Missing required arguments. Specify at least -d directory/path and p YYYY_XXX

mattis@ls4-fe1 /projects/fs1/shared/Test_Jobs/Tiny_Test $
bash ~/Shared/Yggdrasil/bin/delivery.sh -d /projects/fs1/shared/Test_Jobs/Tiny_Test
Error: Missing required arguments. Specify at least -d directory/path and p YYYY_XXX

mattis@ls4-fe1 /projects/fs1/shared/Test_Jobs/Tiny_Test $
bash ~/Shared/Yggdrasil/bin/delivery.sh -d /projects/fs1/shared/Test_Jobs/Tiny_Test -p Tiny_Test
Error: Invalid project ID argument.

mattis@ls4-fe1 /projects/fs1/shared/Test_Jobs/Tiny_Test $
bash ~/Shared/Yggdrasil/bin/delivery.sh -d /projects/fs1/shared/Test_Jobs/Tiny_Test -p 2021_001 -u mattis
The directory is: /projects/fs1/shared/Test_Jobs/Tiny_Test
The project ID is: 2021_001
The LFS_USER is: mattis
The email is: cglu.bioinformatics@scilifelab.se
Adding user `2021_001' to group `ssh_users' ...
Adding user 2021_001 to group ssh_users
Done.
sending incremental file list
Tiny_Test/
Tiny_Test/1.txt
             30 100%    0.00kB/s    0:00:00 (xfr#1, to-chk=9/11)
Tiny_Test/10.txt
             30 100%   29.30kB/s    0:00:00 (xfr#2, to-chk=8/11)
Tiny_Test/2.txt
             30 100%   29.30kB/s    0:00:00 (xfr#3, to-chk=7/11)
Tiny_Test/3.txt
             30 100%   29.30kB/s    0:00:00 (xfr#4, to-chk=6/11)
Tiny_Test/4.txt
             30 100%   29.30kB/s    0:00:00 (xfr#5, to-chk=5/11)
Tiny_Test/5.txt
             30 100%   29.30kB/s    0:00:00 (xfr#6, to-chk=4/11)
Tiny_Test/6.txt
             30 100%   14.65kB/s    0:00:00 (xfr#7, to-chk=3/11)
Tiny_Test/7.txt
             30 100%   14.65kB/s    0:00:00 (xfr#8, to-chk=2/11)
Tiny_Test/8.txt
             30 100%   14.65kB/s    0:00:00 (xfr#9, to-chk=1/11)
Tiny_Test/9.txt
             30 100%    9.77kB/s    0:00:00 (xfr#10, to-chk=0/11)

sent 961 bytes  received 210 bytes  2.34K bytes/sec
total size is 300  speedup is 0.26

mattis@ls4-fe1 /projects/fs1/shared/Test_Jobs/Tiny_Test $
bash ~/Shared/Yggdrasil/bin/delivery.sh -d /projects/fs1/shared/Test_Jobs/Tiny_Test -p 2021_002 -e cglu.bioinformatics@scilifelab.se
The directory is: /projects/fs1/shared/Test_Jobs/Tiny_Test
The project ID is: 2021_002
The LFS_USER is: mattis
The email is: cglu.bioinformatics@scilifelab.se
Adding user `2021_002' to group `ssh_users' ...
Adding user 2021_002 to group ssh_users
Done.
sending incremental file list
Tiny_Test/
Tiny_Test/1.txt
             30 100%    0.00kB/s    0:00:00 (xfr#1, to-chk=9/11)
Tiny_Test/10.txt
             30 100%   29.30kB/s    0:00:00 (xfr#2, to-chk=8/11)
Tiny_Test/2.txt
             30 100%   29.30kB/s    0:00:00 (xfr#3, to-chk=7/11)
Tiny_Test/3.txt
             30 100%   29.30kB/s    0:00:00 (xfr#4, to-chk=6/11)
Tiny_Test/4.txt
             30 100%   29.30kB/s    0:00:00 (xfr#5, to-chk=5/11)
Tiny_Test/5.txt
             30 100%   29.30kB/s    0:00:00 (xfr#6, to-chk=4/11)
Tiny_Test/6.txt
             30 100%   29.30kB/s    0:00:00 (xfr#7, to-chk=3/11)
Tiny_Test/7.txt
             30 100%   14.65kB/s    0:00:00 (xfr#8, to-chk=2/11)
Tiny_Test/8.txt
             30 100%   14.65kB/s    0:00:00 (xfr#9, to-chk=1/11)
Tiny_Test/9.txt
             30 100%   14.65kB/s    0:00:00 (xfr#10, to-chk=0/11)

sent 961 bytes  received 210 bytes  2.34K bytes/sec
total size is 300  speedup is 0.26

mattis@ls4-fe1 /projects/fs1/shared/Test_Jobs/Tiny_Test $
bash ~/Shared/Yggdrasil/bin/delivery.sh -d /projects/fs1/shared/Test_Jobs/Tiny_Test -p 2021_002 -e mattis.knulst@med.lu.se
The directory is: /projects/fs1/shared/Test_Jobs/Tiny_Test
The project ID is: 2021_002
The LFS_USER is: mattis
The email is: mattis.knulst@med.lu.se
The user `2021_002' is already a member of `ssh_users'.
sending incremental file list
Tiny_Test/1.txt
             30 100%    0.00kB/s    0:00:00 (xfr#1, to-chk=9/11)
Tiny_Test/10.txt
             30 100%   29.30kB/s    0:00:00 (xfr#2, to-chk=8/11)
Tiny_Test/2.txt
             30 100%   29.30kB/s    0:00:00 (xfr#3, to-chk=7/11)
Tiny_Test/3.txt
             30 100%   29.30kB/s    0:00:00 (xfr#4, to-chk=6/11)
Tiny_Test/4.txt
             30 100%   29.30kB/s    0:00:00 (xfr#5, to-chk=5/11)
Tiny_Test/5.txt
             30 100%   29.30kB/s    0:00:00 (xfr#6, to-chk=4/11)
Tiny_Test/6.txt
             30 100%   29.30kB/s    0:00:00 (xfr#7, to-chk=3/11)
Tiny_Test/7.txt
             30 100%   14.65kB/s    0:00:00 (xfr#8, to-chk=2/11)
Tiny_Test/8.txt
             30 100%   14.65kB/s    0:00:00 (xfr#9, to-chk=1/11)
Tiny_Test/9.txt
             30 100%   14.65kB/s    0:00:00 (xfr#10, to-chk=0/11)

sent 658 bytes  received 267 bytes  1.85K bytes/sec
total size is 300  speedup is 0.32
chaetognatha commented 1 year ago

TL;DR validation seems to be working and you can specify your own email and that works, unfortunately the default email whether you specify it directly or default to it doesn't seem to work, but that is an issue I need to look more closely at, for now this delivery script has been generalized so we can use it directly

Fattigman commented 1 year ago

Cool, is it on the master branch on Yggdrasil or?

There are some more disussions regarding implementation of delivery, but I think that is a discussion for a separate issue.

chaetognatha commented 1 year ago

Yes on the master branch!

Agreed, I think at some point the delivery script should go in its own repo, just as the demux script that Henning is writing also should have its own repo so that we can isolate them better!

Fattigman commented 1 year ago

Cool, I will start on the changes to this code base to call on the new delivery script.

Fattigman commented 1 year ago

Fixed in https://github.com/ctg-lund/singleCellWorkflows/commit/fca3090c00378d14db2d3218f387304f553af57c

chaetognatha commented 1 year ago

👀