Add vg 1.4.0#5086
Conversation
johanneskoester
commented
Jul 3, 2017
- I have read the guidelines for bioconda recipes.
- This PR adds a new recipe.
- This PR updates an existing recipe.
- This PR does something else (explain below).
LintingYour recipes are in an excellent condition. |
1 similar comment
LintingYour recipes are in an excellent condition. |
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@bgruening this fails because the build requires some git submodules. What is our recommended strategy for such a case (since using the git_url tag is discouraged)? |
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@bgruening @johanneskoester I wanted to add vg some time ago but put it on hold due to dependancy of +20 submodules. Maybe we can do an exception here and use git_url so it could be added? |
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Yes. |
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I think the recommended way is to ask for a release tarball if this is not possible use git_url. |
LintingThe following problems have been found
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LintingYour recipes are in an excellent condition. |
LintingThe following problems have been found
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LintingYour recipes are in an excellent condition. |
…ecipes/vg] Missing dep.
LintingYour recipes are in an excellent condition. |
…ecipes/vg] Missing dep.
LintingYour recipes are in an excellent condition. |
…ecipes/vg] Missing dep.
LintingYour recipes are in an excellent condition. |
LintingThe following problems have been found
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LintingYour recipes are in an excellent condition. |
LintingYour recipes are in an excellent condition. |
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The remaining error seems to be a problem with the compiler version: vgteam/vg#751. We need gcc 4.9 for this to work. |
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The error shows they use |
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https://github.com/vgteam/vg/blame/v1.6.0/README.md#L33:
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Yeah, I had the hope that those patches in devtoolset-2 gcc would help here :-(. |
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Note that with the new compiler packages you have to make sure |
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And you have to use the |
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Seems like protobuf still wants to use gcc... |
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Yes, that is what I will do. Yeah removing the dependencies would be nice indeed... |
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@mbargull I think I am stuck here. Seems like the error is caused by protobuf still not finding g++: protocolbuffers/protobuf#492. Since you have already familiarized with the new compilers, any idea? |
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protobuf's errors -- let's see if adding EDIT: Specifically, this also failed at |
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Hm, conda-forge's recipe for the same version doesn't mention OpenMP, though: https://github.com/conda-forge/protobuf-feedstock/tree/4a47177307485d1ce97cd1af7fb35ccdf6297468/recipe |
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conda-forge's recipe made me curious: looks like they just use the system Why would this be interesting? => If were to change some recipes to explicitly use |
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Yay, that worked perfectly. See ClickHouse/ClickHouse#1002 (comment) for fixes. |
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So regarding that
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Any suggestions @ekg ? |
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Added in another PR |