ubuntu compile fail

[yplee614]

CXXLD prepro CXXLD show-coords CXXLD show-diff CXXLD repeat-match CXXLD mgaps CXXLD delta-filter CXXLD postnuc swig/perl5/swig_wrap.cpp:322:20: fatal error: string.h: No such file or directory compilation terminated. Makefile:1830: recipe for target 'swig/perl5/swig_perl5_mummer_la-swig_wrap.lo' failed make[2]: [swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1 make[2]: Waiting for unfinished jobs.... make[2]: Leaving directory '/home/yplee/raspberry/software/MaSuRCA-3.3.1/global-1/MUMmer' Makefile:2418: recipe for target 'install' failed make[1]: [install] Error 2 make[1]: Leaving directory '/home/yplee/raspberry/software/MaSuRCA-3.3.1/global-1/MUMmer' Makefile:847: recipe for target 'install-special' failed make: [install-special] Error 2

[osowiecki]

Have you installed perl via conda? After fighting with the problem the entire night I just compiled the package on my laptop that doesn't use anaconda.

I blame conda, what's your experience.

gcc and g++ v7.4 perl v5.26.1

[osowiecki]

I was correct. Forcing it to use system libraries instead of conda ones fixed the problem. Check out your .bashrc and make sure it looks for system libraries first. Use perl v5.26.1.

[cement-head]

@osowiecki How do I specify which libraries (system VS conda) to prioritise in the <.bashrc> file?

[osowiecki]

A year has passed. Try using a ready docker image of masurca or create a separate conda environment (conda create -n) and then activate it. If you really want to edit .bashrc, add system paths before conda paths. Libraries found earlier on the list should get priority.

For example :

cat /etc/environment

default system paths

PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games/:/usr/games/"

source /etc/environment

PATH="$PATH:/home/anaconda/anaconda3/bin:/home/anaconda/ShortStack"

https://unix.stackexchange.com/questions/260941/add-path-to-bashrc

[cement-head]

So you're saying mascara is in conda? And I could install it via a separate environment?

[osowiecki]

So you're saying mascara is in conda? And I could install it via a separate environment?

https://anaconda.org/bioconda/masurca

[cement-head]

Fantastic! Thanks!

EDIT: Installing via Conda was very easy & POLCA polished my 6GB frog genome with 500 GB of Illumina PE reads in 12 hours from start to finish (including the BWA stage). Used a stand alone workstation - AMD dual EPYC with 2 TB ECC RAM. Used <-m 15G> in the cli.