Prokka conda install broken.

[Rob-murphys]

I am trying to install Prokka via conda using the recomended channel priority:
conda install -c conda-forge -c bioconda -c defaults prokka

But upon typing prokka -h I get the following error:

Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /home/lamma/miniconda3/envs/annotation/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/lamma/miniconda3/envs/annotation/lib/site_perl/5.26.2 /home/lamma/miniconda3/envs/annotation/lib/5.26.2/x86_64-linux-thread-multi /home/lamma/miniconda3/envs/annotation/lib/5.26.2 .) at /home/lamma/miniconda3/envs/annotation/bin/prokka line 30.
BEGIN failed--compilation aborted at /home/lamma/miniconda3/envs/annotation/bin/prokka line 30.

The conda environment looks as follows:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
aragorn                   1.2.38               h470a237_2    bioconda
barrnap                   0.9                           3    bioconda
bedtools                  2.29.2               hc088bd4_0    bioconda
blast                     2.9.0                h20b68b9_1    bioconda
boost                     1.68.0          py37h8619c78_1001    conda-forge
boost-cpp                 1.68.0            h11c811c_1000    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
certifi                   2019.11.28               py37_0    conda-forge
expat                     2.2.5             he1b5a44_1004    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gnutls                    3.6.5             hd3a4fd2_1002    conda-forge
hmmer                     3.2.1                he1b5a44_2    bioconda
icu                       58.2              hf484d3e_1000    conda-forge
infernal                  1.1.2                h14c3975_2    bioconda
ld_impl_linux-64          2.33.1               h53a641e_7    conda-forge
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_1    conda-forge
libgfortran-ng            7.3.0                hdf63c60_3    conda-forge
libgomp                   9.2.0                h24d8f2e_1    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
libidn11                  1.34                 h1cef754_0    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
libopenblas               0.3.7                h5ec1e0e_6    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_1    conda-forge
minced                    0.4.2                         0    bioconda
ncurses                   6.1               hf484d3e_1002    conda-forge
nettle                    3.4.1             h1bed415_1002    conda-forge
numpy                     1.17.3           py37h95a1406_0    conda-forge
openjdk                   11.0.1            h516909a_1016    conda-forge
openmp_impl               4.5                       0_gnu    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
parallel                  20191122                      0    conda-forge
pcre                      8.43                 he1b5a44_0    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-archive-tar          2.32                    pl526_0    bioconda
perl-bioperl              1.6.924                       4    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-bzip2   2.087           pl526he1b5a44_0    bioconda
perl-compress-raw-zlib    2.087           pl526hc9558a2_0    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-io-compress          2.087           pl526he1b5a44_0    bioconda
perl-io-zlib              1.10                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    bioconda
perl-threaded             5.26.0                        0    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-xml-namespacesupport 1.12                    pl526_0    bioconda
perl-xml-parser           2.44_01         pl526ha1d75be_1002    conda-forge
perl-xml-sax              1.02                    pl526_0    bioconda
perl-xml-sax-base         1.09                    pl526_0    bioconda
perl-xml-sax-expat        0.51                    pl526_3    bioconda
perl-xml-simple           2.25                    pl526_1    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
perl-yaml                 1.29                    pl526_0    bioconda
pip                       19.3.1                   py37_0    conda-forge
prodigal                  2.6.3                h516909a_2    bioconda
prokka                    1.12.partialgenes               0    agbiome
python                    3.7.6                h357f687_2    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
setuptools                44.0.0                   py37_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
tbl2asn                   25.7                          0    bioconda
tk                        8.6.10               hed695b0_0    conda-forge
wheel                     0.33.6                   py37_0    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge

I know this has been an issue before but none of the fixes on previous threads worked plus there were a couple of years old. Any idea how to fix this issue?

[cabrerad]

Try this:
$ conda create -n prokka_env -c conda-forge -c bioconda prokka
$ conda activate prokka_env

It worked for me! I had the same problem as you.

You can check your environment list with:
$ conda env list

[Rob-murphys]

@cabrerad So just omitting the -c default is a fix? @tseemann Any idea why this would be the case?

Edit:
Tried the above and I get the same error. Any suggestions?

[tseemann]

I have no idea, and am unable to support conda itself. Sorry.

[nahanoo]

I had the same issue with

conda install -c conda-forge -c bioconda -c defaults prokka

I was able to resolve this issue by symlinking Version.pm from perl 5.22 which is also pulled by the conda recipe into the perl 5.26 library.

ln -s ~/miniconda3/envs/placeholder/lib/perl5/site_perl/5.22.0/Bio/Root/Version.pm ~/miniconda3/envs/placeholder/lib/5.26.2/ # replace placeholder with your environment name

I hope this helps anyone who stumbles across the same issue.

[xzsword]

It seems you have to download the perl module named Bio::Root::Version. What I do is
perl -MCPAN -e shell
force install Bio::Root::Version
and then prokka could work.

[mroach-awri]

conda seems to install some of the libraries under /lib/site_perl/5.26.2/ and some under /lib/perl5/site_perl/5.22.0 which is fine except it doesn't add the 5.22.0 directory to the PERL5LIB path for the conda environment. You should be able to export a new PERL5LIB path to include it, or my dumb solution:

cd <envpath>/lib/site_perl/5.26.2/
ln -s ../../perl5/site_perl/5.22.0/* .
# ignore all the complaints