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Ensembl / Bio-DB-HTS

Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib
Apache License 2.0
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Not able to compile/install Bio::DB::HTS in conda environment #105

Open zuber-bioinfo opened 1 year ago

zuber-bioinfo commented 1 year ago

I have created an environment for seal and want to link VEP with it. ./vep_install not working. Then, I have manually installed API. added them to PERL5LIB environment specific to conda_prefix. installed gcc, g++, cpanm in conda also. cpanm method is not working, same error. Error as below,

Building Bio::DB::HTS CMD : env HTSLIB_DIR=/tmp/HcSxsEQ4FZ/htslib perl Build.PL /home/genexp/miniconda3/envs/seal/bin/x86_64-conda-linux-gnu-ld: unrecognized option '-Wl,-O2' /home/genexp/miniconda3/envs/seal/bin/x86_64-conda-linux-gnu-ld: use the --help option for usage information Warning: ExtUtils::CBuilder not installed or no compiler detected Proceeding with configuration, but compilation may fail during Build

Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '3.01' Building Bio-DB-HTS Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'. Aborting Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'. Aborting Build test failed. Not continuing at INSTALL.pl line 201. cannot remove path when cwd is /tmp/HcSxsEQ4FZ/Bio-DB-HTS for /tmp/HcSxsEQ4FZ: at /home/genexp/miniconda3/envs/seal/lib/perl5/core_perl/File/Temp.pm line 916.

Please help.

sgiorgetti commented 1 year ago

Hello @zuber-bioinfo - thanks for raising this. From what you posted, I am not sure the issue is related to Bio::DB::HTS. I am under the impression something is not quite right with your environment: it seems the installer/your session cannot find the compiler and/or something is wrong with the linker.

I would suggest to reach out to our Ensembl Outreach team, by following instructions at the following link http://www.ensembl.org/info/about/contact/index.html

Eventually, you'll be redirected to me ;-) but we'll be able to discuss details thoroughly.

Shall keep this issue open to report back results and possibly suggestions.