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ChaissonLab / LRA

Long read aligner
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LRA pre-compiled binaries [question] #13

Open davidebolo1993 opened 3 years ago

davidebolo1993 commented 3 years ago

Hi all,

Thanks for building this software. It looks very promising. Would it be possible to share pre-compiled binaries? While on a recent workstation it works fine, I'm having difficulties installing lra on a (outdated, I must say) SUSE server. Maybe a pre-compiled lra can solve all the issues I'm getting into. Thanks a lot,

Davide

mchaisso commented 3 years ago

Hi Davide - are you able to install bioconda? lra is available there. We can also share binaries, but through conda we can keep you up to date.

On Fri, Feb 5, 2021 at 12:59 AM Davide Bolognini notifications@github.com wrote:

Hi all,

Thanks for building this software. It looks very promising. Would it be possible to share pre-compiled binaries? While on a recent workstation it works fine, I'm having difficulties installing lra on a (outdated, I must say) SUSE server. Maybe a pre-compiled lra can solve all the issues I'm getting into. Thanks a lot,

Davide

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davidebolo1993 commented 3 years ago

Hi @mchaisso,

That's the point. I cannot install lra by manual compilation neither through conda (bio-channel). The issue is somehow related to outdated libraries I cannot upgrade (unfortunately). I managed to solve similar issues with other tools in the past by statically compile on another machine and re-use the binaries on the "old Suse". I'm not entirely sure this is going to work this time, especially if my kernel is too old, but maybe I can give this a try. Thanks a lot!

Davide

danessel commented 3 years ago

same here,

ramsayl commented 3 years ago

Similar issue here, unfortunately. Bioconda is unable to resolve dependencies on an older install.

mchaisso commented 3 years ago

Can you try the precompiled binary in V1.2.0? https://github.com/ChaissonLab/LRA/releases/tag/V1.2.0

ramsayl commented 3 years ago

./lra: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory

libhts is installed, though. (Through Debian apt, default install location /usr/local/lib/libhts.so.3 )

davidebolo1993 commented 3 years ago

@ramsayl, maybe this works for you https://github.com/jfarek/alignstats/issues/2

Jingwen7 commented 3 years ago

Hi @ramsayl ,

can you try export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/ and then ./lra?

mchaisso commented 3 years ago

I'll make the version on bioconda statically linked.

On Mon, Apr 26, 2021 at 12:38 PM Davide Bolognini @.***> wrote:

@ramsayl https://github.com/ramsayl, maybe this works for you jfarek/alignstats#2 https://github.com/jfarek/alignstats/issues/2

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ramsayl commented 3 years ago

./lra: error while loading shared libraries: libdeflate.so.0: cannot open shared object file: No such file or directory

Perhaps a list of dependencies could be put together for non-bioconda installs?