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smithlabcode / preseq

Software for predicting library complexity and genome coverage in high-throughput sequencing.
https://preseq.readthedocs.io
GNU General Public License v3.0
78 stars 16 forks source link

2.0 release tarball does not include smithlab_cpp sources #19

Closed rekado closed 8 years ago

rekado commented 8 years ago

The latest release tarball is not self-contained. While it is good that preseq does not bundle smithlab_cpp, it is not easy to build preseq as there has not been an official release of the smithlab_cpp library.

Just unpacking the tarball and building preseq results in an error:

make: *** No rule to make target '/tmp/nix-build-preseq-2.0.drv-0/preseq-2.0/smithlab_cpp//smithlab_os.o', needed by 'preseq'.  Stop.

In my latest version of the preseq package for GNU Guix I'm first building a prelease of smithlab_cpp and then set SMITHLAB_CPP to the lib output of that package; I also modify the INCLUDEDIRS variable such that the installed headers of the smithlab_cpp package can be found.

If there will be a release for smithlab_cpp soon, it would be nicer if preseq could be linked against that library directly.

timydaley commented 8 years ago

I think I fixed it. If it's not fixed, let me know. I'm leaving this issue open until I'm sure it's fixed. Thank you.

greysAcademicCode commented 8 years ago

It's not fixed.

Look inside the source code release package: https://github.com/smithlabcode/preseq/archive/v2.0.2.tar.gz

You'll see that the smithlab_cpp folder there is empty. I don't think you can expect GitHub to recurse into submodules and fetch the code from them when it's generating the release package.

timydaley commented 8 years ago

Yes, we know that GitHub doesn't include submodules on the release. That's why I included a separate tarball (https://github.com/smithlabcode/preseq/releases/download/v2.0.2/preseq_v2.0.2.tar.bz2) that includes the submodule.