Handle symbolic links to transrate wrapper

blahah / transrate

Understand your transcriptome assembly

http://hibberdlab.com/transrate

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Handle symbolic links to transrate wrapper #177

Closed roryk closed 8 years ago

roryk commented 8 years ago

Hi @Blahah,

Happy holidays to you. This allows a symbolic link to be made to the transrate wrapper and have it get resolved to the correct directory which will let this get made into a bioconda package without mucking anything else up.

roryk commented 8 years ago

This doesn't entirely fix the installation problem, but is a first step. It works locally but fails in the docker image: https://github.com/bioconda/bioconda-recipes/pull/511

roryk commented 8 years ago

transrate --version
/anaconda/envs/_test/share/transrate-1.0.1-0/lib/app/ruby/bin.real/ruby: relocation error: /anaconda/envs/_test/share/transrate-1.0.1-0/lib/librt.so.1: symbol __vdso_clock_gettime, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
TESTS FAILED: transrate-1.0.1-0

blahah commented 8 years ago

@roryk is this ready to review, or would you like the PR left open so you can try to get it working in the docker image? Happy to try to help with the latter.

roryk commented 8 years ago

Hi @Blahah,

The symbolic link fix would be useful to merge in. I'd love some help with the docker issue, I kind of stalled out figuring out what was wrong.