Failing to compile kent utilities due to openSSL dependencies

Question

[4galaxy77]

I would like to use the LOFTEE plugin for VEP on a cluster with no root permissions, but it fails with this error:

WARNING: Failed to compile plugin LoF: Can't locate Bio/DB/BigWig.pm in @INC (you may need to install the Bio::DB::BigWig module) (@INC contains: /home/samm/projects/vep_annotation/plugins/loftee /home/samm/miniconda3/envs/vep/share/ensembl-vep-108.2-0/modules /home/samm/miniconda3/envs/vep/share/ensembl-vep-108.2-0 /home/samm/miniconda3/envs/vep/lib/perl5/5.32/site_perl /home/samm/miniconda3/envs/vep/lib/perl5/site_perl /home/samm/miniconda3/envs/vep/lib/perl5/5.32/vendor_perl /home/samm/miniconda3/envs/vep/lib/perl5/vendor_perl /home/samm/miniconda3/envs/vep/lib/perl5/5.32/core_perl /home/samm/miniconda3/envs/vep/lib/perl5/core_perl .) at /home/samm/projects/vep_annotation/plugins/loftee/gerp_dist.pl line 2.
BEGIN failed--compilation aborted at /home/samm/projects/vep_annotation/plugins/loftee/gerp_dist.pl line 2.
Compilation failed in require at /home/samm/projects/vep_annotation/plugins/loftee/LoF.pm line 27.
Compilation failed in require at (eval 42) line 2.
BEGIN failed--compilation aborted at (eval 42) line 2.

So I then go to install Bio::DB::BigWig, but this requires the installation of the Kent source tree...

So I go to install the Kent source tree, following these instructions:

cd $KENT_SRC/lib
echo 'CFLAGS="-fPIC"' > ../inc/localEnvironment.mk

make clean && make

gcc -O -g "-fPIC" -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_SSL   -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/include -I/usr/include/libpng15  -o hmac.o -c hmac.c
hmac.c:12:10: fatal error: openssl/hmac.h: No such file or directory
   12 | #include "openssl/hmac.h"
      |          ^~~~~~~~~~~~~~~~
compilation terminated.
make: *** [hmac.o] Error 1

I installed openSSL into the conda vep environment:

 mamba install -c anaconda openssl -n vep

But this still fails.

This is driving me nuts. Surely there has to be an easier way than manually installing perl modules (vomit)? If not, how can I compile the kent source tree against the openSSL lib using conda? Am I doing something trivially wrong here?

[barslmn]

You need the development branch when compiling. Try libssl-dev package if you're on debian based distribution.