Helixer update (version 0.3.6)

[rlibouba]

Hello,
I am opening this PR to update Helixer.
There are three new parameters compared to the previous version in this directory: --compression, --no-multiprocess, and --write-by. In addition, there are corrections to the tool in certain points.

Thank you. Have a nice day!
Romane

[rlibouba]

I fixed the problem with helixer_post_bin. Another problem I encountered is that the output generated by the tests is empty, but it shouldn't be.

[rlibouba]

Hi,

I am encountering this error: Error: helixer_post_bin not found in $PATH, this is required for Helixer.py to complete.

I first tried adding helixer_post_bin to the path to fix the error, but it didn't work. I looked at the issues on this directory. An issue with the same error was mentioned. Users using Singularity or Docker had the same issue. Some people modified the dockerfile to fix the error. I was able to test it, and it worked. A PR with modifications to the dockerfile was opened. I added a comment to mention that with modifications to the dockerfile, my tests for updating the tool on Galaxy worked. I am waiting for feedback from the developers.

[rlibouba]

Hello, the issue with the docker image has been resolved and the tests are passing. It is ready to be reviewed.
Thank you. Have a good day.

[mvdbeek]

Awesome, would love to see this merged!

[abretaud]

Gogogo! thanks @rlibouba!