perl-bioperl recipe not working on Linux

[mkweskin]

The perl-bioperl recipe is not installing a functional copy of bioperl on Linux.

(base) $ conda create -n bioperl -c conda-forge -c bioconda -c defaults perl-bioperl
...
The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-0_gnu
  libgcc             conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2
  libgomp            conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2
  perl               conda-forge/linux-64::perl-5.26.2-h516909a_1006
  perl-bioperl       bioconda/linux-64::perl-bioperl-1.6.924-4
  perl-threaded      bioconda/linux-64::perl-threaded-5.26.0-0
  perl-yaml          bioconda/noarch::perl-yaml-1.29-pl526_0
...
(base) $ conda activate bioperl
(bioperl) $ echo "use Bio::Seq;" | perl
Can't locate Bio/seq.pm in @INC (you may need to install the Bio::seq module) (@INC contains: /home/user/miniconda3/envs/bioperl/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/user/miniconda3/envs/bioperl/lib/site_perl/5.26.2 /home/user/miniconda3/envs/bioperl/lib/5.26.2/x86_64-linux-thread-multi /home/user/miniconda3/envs/bioperl/lib/5.26.2 .) at - line 1.
BEGIN failed--compilation aborted at - line 1.

I noticed it was installing perl-bioperl-1.6.924-4 so I also tried 1.7.2:
conda create -n bioperl-1.7.2 -c conda-forge -c bioconda -c defaults "perl-bioperl>=1.7.2" and got the same perl error message. (Edit: actually this produces a working version of bioperl, see replies below.)

The above tests were on Linux. On Mac, perl-bioperl 1.7.2 seems to work.

Thanks and apologies if this is not the correct place to report this type of issue.

[tseemann]

I concur something is not right - see tseemann/berokka#26

But i think it was fixed here #20286

I had to set perl >=5.26 and perl-bioperl >=1.7.2 ?

[mkweskin]

What @tseemann suggested worked for me.

I am revising what I wrote in my original message. In trying again, conda create -n bioperl-1.7.2 -c conda-forge -c bioconda -c defaults "perl-bioperl>=1.7.2" does produce a bioperl install that works.

I'm not sure why the newest version of the perl-bioperl module is not used by default.
@tseemann you're more experienced with conda packages than me. Is there something that can be done so that perl-bioperl installs 1.7.2 by default instead of the older 1.6.924-4? Otherwise I will close this issue.

[alanhoyle]

I'm running into this problem. I'm trying to update a conda-based Docker image. the old image was based on continuumio/miniconda and I'm trying to update it to be based on continuumio/miniconda3 to use python3 instead of python2.

Among the things I am trying to install is ensembl-vep=103.1, which requires perl-bioperl>=1.7.2

#8 4.902   - package ensembl-vep-103.1-pl5262h4a94de4_1 requires perl-bioperl >=1.7.2, but none of the providers can be installed

If I try to have conda install perl-bioperl=1.7.2:

 #8 3.705   - package perl-bioperl-1.7.2-pl526_10 requires perl-bio-tools-run-alignment-tcoffee, but none of the providers can be installed

If I try to have conda install perl-bio-tools-run-alignment-tcoffee
#7 3.884 - package perl-bio-tools-run-alignment-tcoffee-1.7.4-pl526_0 requires t_coffee, but none of the providers can be installed

I note that there's packages for t_coffee and t-coffee out there in bioconda land.

The former won't install:

 #8 3.475   - package t_coffee-11.0.8-py37hea885bf_8 requires python >=3.7,<3.8.0a0, but none of the providers can be installed 

I checked, and my python is 3.8.5.

t-coffee DOES install, but doesn't satisfy the t_coffee dependency.

Here's the Dockerfile I'm using

Dockerfile.txt

Note that I get similar errors if I try to use conda instead of mamba or if I try to use continuumio/miniconda3 as the Docker base image.