Tag a new release - Githubissues

cbg-ethz / haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

GNU General Public License v3.0

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Tag a new release #54

Closed DrYak closed 6 years ago

DrYak commented 6 years ago

Hi @armintoepfer !

Would you (or anybody else with the necessary access rights enabled) mind tagging a v1.0.2 release of the latest commits currently in master so I can try to make a bioconda recipe out of them ?

Thanks a lot in advance !

DrYak commented 6 years ago

Also, it would be great if you could include a LICENSE file together with that release, like @SoapZA did for small genome utilities.

DrYak commented 6 years ago

By the way, I've found the following fix seems to be needed on older versions of GCC :

sed -i '/#define .*_H_/a#include <memory>' src/{AlignmentRecord,HistogramBasedDistribution}.

Without this, the definition of std::unique_ptr is missing in a few places. I'll make a pull request shortly.

Also, a bioconda specific-fix:

sed -ri 's@#include <regex>@#include <boost/regex.hpp>@;s/std::(s?regex|smatch)/boost::\1/g' src/docopt/docopt.cpp

bioconda ships only with version 4.8.x of GCC (probably because of CentOS 7). But as reported by dpcopt's readme, GCC 4.8.x's regex is broken, and only fixed in 4.9.0 so the build script I'm writing will force a switch to Boost's regex (which is a super-set of C++11's regex) in this specific situation.

It has nothing to do with Haploclique. Hapoclique is working correctly as it should, so there is no reason to modify it.

DrYak commented 6 years ago

Here's the pull request I need before 1.0.2 is tagged, in order to be able to make a bioconda recipe.

DrYak commented 6 years ago

i'm still not ready with my C++11 -> Boost "regex engine swap" : I'm getting exceptions thrown from within docopt due to (char *)NULL to std::string conversions.

I'll investigate further next week.

(so no tagging for now...)

armintoepfer commented 6 years ago

I inc'd to v1.3.0 and tagged.

DrYak commented 6 years ago

Thanks. I'll try to find fixes around the thrown exceptions (maybe a few more fixes pulling will be needed) And we should be set and ready for bioconda.

DrYak commented 6 years ago

Yet another pull request necessary before a successful bioconda recipe. It has two changes :

first is upgrading docopt which fixes bugs (and simplifies using the old regex-less GCC 4.8 still used by bioconda).
second is changing behavious of -h as required by bioconda recipes' tests.

DrYak commented 6 years ago

Bioconda recipe is fully functional after that (at least it passes the unit tests)