Fix repeatmodeler recipe

[Juke34]

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[Juke34]

This change should fix the problem with this recipe.

[Juke34]

@BiocondaBot please add label

[marcelm]

Which problem does this PR address? Why do the current tests not catch that problem? Can you add a test that would fail with the current version of the recipe, but would pass with the change proposed in this PR?

[marcelm]

If those tests are hard to write then you should at least verify manually that the patch actually fixes the problem. You can use the fetch artifacts command, for example, and then install the revised package locally.

[Juke34]

Which problem does this PR address?

It has been a while this recipe is not working, it is like an empty shell. The tool seems to run but do not perform anything useful. ie (#9988, Dfam-consortium/RepeatModeler#21, https://www.biostars.org/p/368150/, etc...).

The current test just check actually the main tool compile. But RepeatModeler is a pack of several tools coming with RepatModeler plus several tools from external resources. If one of them fail the pipeline doesn't crash it just skip steps. Depending the crash the output could be empty or not, but we get a file (consensi.fa). The thing is to test the whole pipeline we need to include a data set and run RepeatModeler on it, that could run for hours...

[Juke34]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
linux-64	repeatmodeler-1.0.11-pl526_2.tar.bz2	repodata.json

---

You may also use conda to install these:

• For packages on linux-64:

conda install -c https://86231-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	Install with docker
repeatmodeler	1.0.11--pl526_2	show curl "https://86231-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/repeatmodeler%3A1.0.11--pl526_2.tar.gz" | gzip -dc | docker load

[Juke34]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
linux-64	repeatmodeler-1.0.11-pl526_2.tar.bz2	repodata.json

---

You may also use conda to install these:

• For packages on linux-64:

conda install -c https://86312-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	Install with docker
repeatmodeler	1.0.11--pl526_2	show curl "https://86312-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/repeatmodeler%3A1.0.11--pl526_2.tar.gz" | gzip -dc | docker load

[Juke34]

I have added a test now. The test file is 300kb but I cannot make it smaller. The tool needed a fait amount of data to produce a useful output we can check. A least it will avoid to have the problem we got until now where people were trying to use a recipe that was not really working.

[dpryan79]

@bioconda-bot please merge

I'm not overly enthused about a 300kb test file, but it looks like this is the only way currently to prevent regression in this recipe.

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

[oushujun]

Thanks for fixing this. Has this updated to RepeatModeler2 yet?

[Juke34]

Not yet... at least not by me.

[jebrosen]

I have a bit of a backlog, but updating the RepeatMasker and RepeatModeler recipes is still on my radar.

[oushujun]

@Juke34 OK that's good to know. I saw your other post (#19805), RECON and RepeatScout is still not available to OSX yet. @jebrosen Are these also on your radar? Thanks guys!

[Juke34]

Done