porechop: Use the standard release

[sjackman]

A special tag of Porechop was made to support older versions of GCC.
Use the standard release with a recent version of GCC.

• I have read the guidelines for bioconda recipes.
• This PR updates an existing recipe.

[sjackman]

See #7436
and rrwick/Porechop#41

[sjackman]

CircleCI failed with…

    g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -c -o porechop/src/alignment.o porechop/src/alignment.cpp
    g++: error: unrecognized command line option ‘-std=c++14’

https://circleci.com/gh/bioconda/bioconda-recipes/29983

I thought that Bioconda was using GCC 7 now. Am I mistaken?

[bgruening]

@sjackman we migrated to conda-build 3 which makes the configuration of the default compiler possible/easier. You just need to add https://github.com/bioconda/bioconda-recipes/blob/master/recipes/delly/conda_build_config.yaml to your recipe. We will switch to this by default as soon as conda-forge is rebuild.

[sjackman]

Thanks, Björn. I've added conda_build_config.yaml.

[sjackman]

CircleCI on Linux

    porechop/include/seqan/system/file_sync.h: In member function 'bool seqan::File<seqan::Sync<TSpec> >::openTemp(int)':
    porechop/include/seqan/system/file_sync.h:337:25: error: call of overloaded 'empty(std::__cxx11::string&)' is ambiguous
             if (empty(tmpDir))
                             ^

https://circleci.com/gh/bioconda/bioconda-recipes/30016

[sjackman]

Looks like we make be stuck and Porechop 0.2.3 compiles with neither GCC 4 nor GCC 7. It does build with GCC 5. Is that an option, to build with GCC 5?

[bgruening]

No, there are only those two. Sorry.

[sjackman]

Hmm. We could update the bundled version of Seqan to a recent release, or I could abandon this PR. Since its purpose was to tidy up the formula, I'm inclined to abandon this PR.
I've opened an upstream bug report. rrwick/Porechop#76