GitLab

doc/.gitlab-ci.yml: build doc with Docker, also on 'feature-a/release' branches

See merge request !680

vidjil-algo: release 2020.05

See merge request !683

see #4278

see #4274

follows 13501a70

Correct trimSequence

Closes #4272

See merge request !681

Bug remained in some cases because of a poor initial test case

Fix #4272 (and #4263)

Feature a/docker benchmark

See merge request !678

vidjil-algo: release 2020.04

See merge request !674

see #4268

Mikaël Salson authored Apr 28, 2020 and Mathieu Giraud committed Apr 28, 2020

If we try to set the same index several times we will wrongly have several references to it and, thus,
will never be deleted, which Valgrind dislikes

See !674

see #4268

Feature a/small fixes

See merge request !677

--gz makes also output .vdj.fa.gz

Closes #4270

See merge request !676

Reset the seed to have the same conditions. Otherwise depending on the number of tests and the number of times
the pseudo-random generator has been used the test may fail or succeed (we are using a RandomScore now)

We didn't take into account the length (as it was added later). This is now fixed.

closes #4270

see #4270

opens #4270

--gz makes also output AIRR .tsv.gz

Closes #4249

See merge request !675

Our main file is .vijdil, and not anymore .vdj.fa (for ages)

closes #4249

see #4269

opens #4269

Fix algo with N in window

Closes #4263

See merge request !672

For some reason it was failing with my g++-5

As trimSequence is used on a representative and as the representative should contain the window we now
make sure that the window is not trimmed.

Fix #4263

No more need to launch scripts from scripts directory

See merge request !670

vidjil-algo: new option --gz to output .vidjil.gz

Closes #4253

See merge request !667

Docker emails

Closes #2760

See merge request !666

Mikaël Salson authored Apr 23, 2020 and Vidjil Team committed Apr 23, 2020

server/web2py/applications/vidjil/scripts/*.sh: No more need to launch scripts from the scripts/ directory

Now we can launch the script from anywhere. With Docker we can even launch a script from the host using docker exec.