Update unicycler to v0.4.6

[corburn]

• I have read the guidelines for bioconda recipes.
• This PR adds a new recipe.
• AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
• This PR updates an existing recipe.
• This PR does something else (explain below).

[bgruening]

we could actually try to build this recipe now by overwriting the default compilers and using the new once

[bgruening]

@corburn are you planning to work on this?

[PertuyF]

@corburn I had a look at the errors, it seems come calls to the overload function seqan::empty are ambiguous, likely with std::empty but I'm really not sure here. Anyway, this issue could be linked to our problem, do you see a solution in there?

[corburn]

@bgruening not today, but as time permits yes. I mentioned I don't yet know how to fix the recipe, but I haven't given up on it. I am comfortable with anyone working on the same recipe and submitting a successful pull request before me. If you think I should be doing something differently, please let me know.

I recently found a clue why I have not been able to use the bioconda-utils-build-env docker container on my local system. The underlying image of the bioconda-utils-build-env is centos:6 which fails on my kernel: docker/for-linux#58. If the fix from one of the comments resolves the issue, it may make offline debugging easier.

@PertuyF thanks for the link, I'll check it out and keep you posted.

[bgruening]

I looped in the seqan devs and they recommended to update to seqan 2.4. Seqan should be compatible with 2.3. so all what is needed is replacing the folder ... we should do this here in the recipe and give it a try. If it works we could upstream the changes?

[corburn]

Thanks for tracking that down @bgruening. I'll fix the zlib error tomorrow. If it builds I'll send a pull request upstream.

[corburn]

What is triggering these constraints?

5e83093

Unsatisfiable dependencies for platform linux-64: {'unicycler==0.4.6=py37hdbcaa40_0'}

79b2721

Unsatisfiable dependencies for platform linux-64: {'readline=6.2', 'sqlite=3.13', "python[version='>=3.7,<3.8.0a0']", 'tk=8.5'}

[PertuyF]

No idea for 5e83093, but the latest 79b2721 conflict looks specific to python 3.7 and readline and/or ncurses.
There's some more details if I try to solve an environment with these requirements:

$ conda create -n test 'readline=6.2' 'sqlite=3.13' "python[version='>=3.7,<3.8.0a0']" 'tk=8.5'
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - python[version='>=3.7,<3.8.0a0'] -> ncurses[version='>=6.1,<6.2.0a0']
  - python[version='>=3.7,<3.8.0a0'] -> readline[version='>=7.0,<8.0a0']
  - readline=6.2

Use "conda info <package>" to see the dependencies for each package.

Do you know where the pinning of readline to 6.2 comes from?
Maybe we could skip py37 to test if build is OK with py36 at least?

[bgruening]

anaconda.com is back and it turned green after a restart! Great work @corburn!

[PertuyF]

Good work! @corburn

[druvus]

Cool, great work

[corburn]

Thanks for all the help!