Bioconda

[Smeds]

Would it be possible to have primerclip on bioconda? https://bioconda.github.io/contributing.html

[irishjonathan]

Hi Smeds,

I didn’t know that haskell packages can be added to bioconda (cool). I’ll look into the guidelines a bit more. Probably yes.

Thanks for bringing this up.

-Jon

On Nov 12, 2018, at 3:38 AM, Smeds notifications@github.com wrote:

Would it be possible to have primerclip on bioconda? https://bioconda.github.io/contributing.html

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[Smeds]

Any thoughts on when you will have time to make a recipe for bioconda?

[irishjonathan]

Hi Smeds,

While I can't commit to anything definite, I'll see if I can get primerclip up on bioconda over the weekend. I'll let you know how it goes.

-Jon

On Fri, Feb 22, 2019 at 9:10 AM Smeds notifications@github.com wrote:

Any thoughts on when you will have time to make a recipe for bioconda?

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[willemdek11]

Hi Smeds,

Did you manage to get it in bioconda in the meanwhile?

[willemdek11]

@irishjonathan

[Smeds]

I haven't looked into it, but can do that. Would it be possible make a release/tag primerclip so that I can refer to a version? @willemdek11 @irishjonathan

[irishjonathan]

Release v0.3.8 created. I've only started to dig into the bioconda documentation, any help with adding primerclip would be appreciated.

@willemdek11 @Smeds

[Smeds]

Which license type should I set? @irishjonathan

[Smeds]

I have some problem compiling the source code. It get the followin gerror:

stack build
...
Configuring primerclip-0.3.8...
Warning: For packages using 'cabal-version: >= 1.10' the 'extensions' field is
deprecated. The new 'default-extensions' field lists extensions that are used
in all modules in the component, while the 'other-extensions' field lists
extensions that are used in some modules, e.g. via the {-# LANGUAGE #-}
pragma.                   
primerclip          > build (lib + exe)
Preprocessing library for primerclip-0.3.8..
Building library for primerclip-0.3.8..
[1 of 1] Compiling Lib    

/home/vagrant/primerclip/src/Lib.hs:1661:19: warning: [-Wdeprecations]
    In the use of type constructor or class ‘Sink’
    (imported from Conduit, but defined in conduit-1.3.0:Data.Conduit.Internal.Conduit):
    Deprecated: "Use ConduitT directly"
     |                    
1661 | calcTrimmedPct :: P.Sink AlignedRead (P.ResourceT IO) Double
     |                   ^^^^^^
Preprocessing executable 'primerclip' for primerclip-0.3.8..
Building executable 'primerclip' for primerclip-0.3.8..
[1 of 1] Compiling Main   
Linking .stack-work/dist/x86_64-linux-tinfo6/Cabal-2.0.1.0/build/primerclip/primerclip ...
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_mutex_init.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_mutex_destroy.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_cond_init.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_cond_destroy.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_cond_wait.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_cond_wait.o)(.note.stapsdt+0x64): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_cond_signal.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_cond_broadcast.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_mutex_cond_lock.o)(.note.stapsdt+0x14): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_mutex_cond_lock.o)(.note.stapsdt+0x64): error: relocation refers to local symbol "" [2], which is defined in a discarded section
/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libpthread.a(pthread_mutex_cond_lock.o)(.note.stapsdt+0xb0): error: relocation refers to local symbol "" [2], which is defined in a discarded section
collect2: error: ld returned 1 exit status
`gcc' failed in phase `Linker'. (Exit code: 1)
Completed 51 action(s).   

--  While building package primerclip-0.3.8 using:
      /home/vagrant/.stack/setup-exe-cache/x86_64-linux-tinfo6/Cabal-simple_mPHDZzAJ_2.0.1.0_ghc-8.2.2 --builddir=.stack-work/dist/x86_64-linux-tinfo6/Cabal-2.0.1.0 build lib:primerclip exe:primerclip --ghc-options " -fdiagnostics-color=always"
    Process exited with code: ExitFailure 1

Any idea what could be wrong? @irishjonathan

[Smeds]

I saw that @willemdek11 push a recipe that copies the binary instead of compiling, will therefore stop my attempt to be able to compile primerclip during bioconda installation.