Open c-leber opened 4 years ago
Hi @c-leber ,
You will need to install the missing perl modules, in this case Bio
. Try something like cpanm install Bio::Root::Version
. If you get a new error message on running prokka
after installation of the missing perl module, try cpanm install the::next::missing::module
.
Good luck,
Hi @schultzm ,
I appreciate the reply!
I tried installing as you advised, and ran into more issues:
cpanm install Bio::Root::Version
install is up to date. (0.01)
--> Working on Bio::Root::Version
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.7.tar.gz ... OK
Configuring BioPerl-1.7.7 ... OK
==> Found dependencies: XML::LibXML, XML::LibXML::Reader, DB_File, Test::Memory::Cycle
--> Working on XML::LibXML
Fetching http://www.cpan.org/authors/id/S/SH/SHLOMIF/XML-LibXML-2.0205.tar.gz ... OK
==> Found dependencies: Alien::Libxml2
--> Working on Alien::Libxml2
Fetching http://www.cpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.16.tar.gz ... OK
Configuring Alien-Libxml2-0.16 ... OK
Building and testing Alien-Libxml2-0.16 ... FAIL
! Installing Alien::Libxml2 failed. See /home/ubuntu/.cpanm/work/1599085734.26465/build.log for details. Retry with --force to force install it.
! Installing the dependencies failed: Module 'Alien::Libxml2' is not installed
! Bailing out the installation for XML-LibXML-2.0205.
--> Working on DB_File
Fetching http://www.cpan.org/authors/id/P/PM/PMQS/DB_File-1.853.tar.gz ... OK
Configuring DB_File-1.853 ... OK
Building and testing DB_File-1.853 ... FAIL
! Installing DB_File failed. See /home/ubuntu/.cpanm/work/1599085734.26465/build.log for details. Retry with --force to force install it.
--> Working on Test::Memory::Cycle
Fetching http://www.cpan.org/authors/id/P/PE/PETDANCE/Test-Memory-Cycle-1.06.tar.gz ... OK
Configuring Test-Memory-Cycle-1.06 ... OK
==> Found dependencies: PadWalker
--> Working on PadWalker
Fetching http://www.cpan.org/authors/id/R/RO/ROBIN/PadWalker-2.3.tar.gz ... OK
Configuring PadWalker-2.3 ... OK
Building and testing PadWalker-2.3 ... FAIL
! Installing PadWalker failed. See /home/ubuntu/.cpanm/work/1599085734.26465/build.log for details. Retry with --force to force install it.
! Installing the dependencies failed: Module 'PadWalker' is not installed
! Bailing out the installation for Test-Memory-Cycle-1.06.
! Installing the dependencies failed: Module 'DB_File' is not installed, Module 'XML::LibXML::Reader' is not installed, Module 'XML::LibXML' is not installed, Module 'Test::Memory::Cycle' is not installed
! Bailing out the installation for BioPerl-1.7.7.
I then tried installing these individual dependencies with --force
as described in the output. However, this led to even more failed installs and more dependencies asking for individual install with --force
Any additional ideas?
How about installing BioPerl using conda
conda install -c bioconda perl-bioperl
Hi @nigyta ,
Thanks for the response.
I tried installing BioPerl using conda. It installs successfully, but I still have the same issues with Bio::Root::Version still not being located, or able to be installed.
Searching through the various logs, I was able to resolve some issues by installing make and gcc_linux-64 via conda. Some dependencies, especially DB_File, are still not installing, due to missing libdb-dev. I tried installing libdb via conda, and this did not help. I then installed libdb-dev via apt install, which is successful, but is still said to be missing when I try to install DB_File.
So at this time, it appears to be an issue with libdb-dev being installed, but not being found.
I tried to install prokka to a clean conda environment on Mac, but I got the same error.
Can't locate Bio/Root/Version.pm in @INC ...
I found a similar issue here https://github.com/bioconda/bioconda-recipes/issues/10277 This may help
Hi @nigyta ,
So I followed the suggestion here: [https://github.com/bioconda/bioconda-recipes/issues/10277#issuecomment-470291356_] And downgraded my perl install to version 5.22
This resulted in a message saying XML::Simple was missing, which I was able to fix with conda install -c bioconda perl-xml-simple
prokka now responds positively when I call to it via prokka
Going to grab some files now - hopefully it runs successfully! Will report back tomorrow.
Maybe you can get into the perl environment by perl -MCPAN -e shell force install {related module} my prokka works by this way.
I tried everything that was said.
Changing variables - YES
**) what helped in the end is setting the environment variable as:
export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/
To make this permanent in your conda environment, use:
conda env config vars set PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/ -n [env_name]
MAKE SURE PERL 5.22 IS ALREADY INSTALLED (I think it automatically is with prokka but am not 100% sure)
Downgrading perl - NO 1) Downgrading perl by installing it in the environment did not actually downgrade it because of all the dependencies 2) Perl can only be downgraded by creating a new environment, but it gave me the same error
Installing with cpan/m - NO 1) Did not work when I tried with the cpan shell, either the system's or the specific environment's, and neither when I used cpan or reinstalled cpanminus from conda.
This is actually a problem I saw with a bunch of other programs (just google Bio::Root::Version and you'll get plenty of github results)
Are there any updates on the issue? I've got a very same problem.
I tried everything that was said.
Changing variables - YES **) what helped in the end is setting the environment variable as:
export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/
To make this permanent in your conda environment, use:conda env config vars set PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/ -n [env_name]
MAKE SURE PERL 5.22 IS ALREADY INSTALLED (I think it automatically is with prokka but am not 100% sure)
Downgrading perl - NO
- Downgrading perl by installing it in the environment did not actually downgrade it because of all the dependencies
- Perl can only be downgraded by creating a new environment, but it gave me the same error
Installing with cpan/m - NO
- Did not work when I tried with the cpan shell, either the system's or the specific environment's, and neither when I used cpan or reinstalled cpanminus from conda.
This is actually a problem I saw with a bunch of other programs (just google Bio::Root::Version and you'll get plenty of github results)
Thank you very much! The way changing variables worked!
I tried everything that was said.
Changing variables - YES **) what helped in the end is setting the environment variable as:
export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/
To make this permanent in your conda environment, use:conda env config vars set PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/ -n [env_name]
MAKE SURE PERL 5.22 IS ALREADY INSTALLED (I think it automatically is with prokka but am not 100% sure)
Downgrading perl - NO
- Downgrading perl by installing it in the environment did not actually downgrade it because of all the dependencies
- Perl can only be downgraded by creating a new environment, but it gave me the same error
Installing with cpan/m - NO
- Did not work when I tried with the cpan shell, either the system's or the specific environment's, and neither when I used cpan or reinstalled cpanminus from conda.
This is actually a problem I saw with a bunch of other programs (just google Bio::Root::Version and you'll get plenty of github results)
Thank you for the solution, nothing else worked for me
Hi @nigyta ,
So I followed the suggestion here: [https://github.com/[bioconda/bioconda-recipes/issues/10277](https://github.com/bioconda/bioconda-recipes/issues/10277)#issuecomment-470291356_] And downgraded my perl install to version 5.22
This resulted in a message saying XML::Simple was missing, which I was able to fix with
conda install -c bioconda perl-xml-simple
prokka now responds positively when I call to it via
prokka
Going to grab some files now - hopefully it runs successfully! Will report back tomorrow.
h
I'm having the same issue (in a somewhat specialized setup - Docker container I'm building in WSL to run a snakemake pipeline including prokka) - downgrading Perl doesn't work due to dependencies, installing Bio::Root::Version gives many of the same errors @c-leber had, installing bioperl with the version fixed to 1.7.2 as suggested in #566 also clashes with dependencies and aiming for >=1.7.2 still leads to the same issues.
Hi, This solved the problem for me :
which prokka
)#use lib "$FindBin::RealBin/../perl5"; # for bundled Perl modules
Hope this helps.
I get this error too. bioperl
, perl-xml-simple
are already installed.
Can you send the result of conda list? I suspect an older version of bioperl is installed.
Make sure you have version 1.7.2 installed.
Conda had installed 1.6. Apparently, because I also wanted to install Roary
in the same environment, which apparently needs version 1.6. It is strange that I had both programs running in the same environment before.
This worked:
mamba create -y -c anaconda -c bioconda prokka pandas seaborn ipykernel perl-bioperl==1.7.2 -n prokka
This does not:
mamba create -y -c anaconda -c bioconda prokka pandas seaborn ipykernel perl-bioperl==1.7.2 roary -n prokka
Dependency install can be problematic. Not isolated to conda. Can you try to upgrade?
You are fast. I was still editing the post :-)
I'm having the same issue (in a somewhat specialized setup - Docker container I'm building in WSL to run a snakemake pipeline including prokka) - downgrading Perl doesn't work due to dependencies, installing Bio::Root::Version gives many of the same errors @c-leber had, installing bioperl with the version fixed to 1.7.2 as suggested in #566 also clashes with dependencies and aiming for >=1.7.2 still leads to the same issues.
Hello dear friend.
Kindly try out this command: conda install -c biobuilds perl=5.22 provided by carissableker https://github.com/bioconda/bioconda-recipes/issues/10277
I sorted out this issue of dependencies at once.
I'm having the same issue (in a somewhat specialized setup - Docker container I'm building in WSL to run a snakemake pipeline including prokka) - downgrading Perl doesn't work due to dependencies, installing Bio::Root::Version gives many of the same errors @c-leber had, installing bioperl with the version fixed to 1.7.2 as suggested in #566 also clashes with dependencies and aiming for >=1.7.2 still leads to the same issues.
Hello dear friend.
Kindly try out this command: conda install -c biobuilds perl=5.22 provided by carissableker bioconda/bioconda-recipes#10277
I sorted out this issue of dependencies at once. This worked for my device actually, and I really wonder why I have missed some dependencies since I did use prokka very a few weeks ago.
Adding the conda --no-channel-priority
option resulted in a seemingly-functional most-recent version of prokka in my environment:
$ conda create --no-channel-priority -c conda-forge -c bioconda -n prokka prokka
...
$ source activate prokka
(prokka) $ prokka --version
prokka 1.14.6
(prokka) $ prokka plasmid.fna
...
[15:07:36] Share and enjoy!
thanks @sorenwacker
mamba create -y -c anaconda -c bioconda prokka pandas seaborn ipykernel perl-bioperl==1.7.2 -n prokka
this worked for me on a ubuntu 18 machine after failing with other methods too would be nice to add this to the main ReadMe for others!
Started an AWS Ubunutu 18.04 server. Installed python. Installed miniconda. Ran
conda install -c conda-forge -c bioconda -c defaults prokka
No apparent issues with install.Try running
prokka
Output: Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /home/ubuntu/miniconda3/bin/../perl5 /home/ubuntu/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/lib/site_perl/5.26.2 /home/ubuntu/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/lib/5.26.2 .) at /home/ubuntu/miniconda3/bin/prokka line 32. BEGIN failed--compilation aborted at /home/ubuntu/miniconda3/bin/prokka line 32.Thoughts?