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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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Missing perl LWP::Simple dependency #71

Open brymerr921 opened 5 years ago

brymerr921 commented 5 years ago

Hi,

I've installed metawrap on several computer systems. On most systems it works great, and on others it says that for MaxBin (binning module), the perl dependency LWP::Simple can't be found in the @INC path (also see issue #17). The fix I found for this is: 

conda install -c bioconda perl-lwp-simple

It may be useful to include this in your conda package. Thanks for the great wrapper!

Bryan

ursky commented 5 years ago

Thanks for the tip, I will include perl-lwp-simple as a dependency. The current (metaWRAP v=1.0.3) implementation has other issues with MaxBin2, however. Another user pointed out that the shebang in MaxBin points to the system perl, not miniconda's perl. This causes a lot of dependency problems... I plan to push metaWRAP v=1.0.4 today, which should fix both issues. Hopefully this wont make a few more in the process...

brymerr921 commented 5 years ago

I manually changed my shebang line within the run_MaxBin.pl script and it didn't seem to break anything else. Thanks!

ursky commented 5 years ago

The newest version should have the correct shebang.

kalonji08 commented 2 years ago

Hi @ursky I'm having the same issue i installed conda install -c bioconda perl-lwp-simple but nothing still here is the code?

rocessing KRI_R.bam depth file... Can't locate LWP/Simple.pm in @INC (you may need to install the LWP::Simple module) (@INC contains: /home/kalonjilab/miniconda3/envs/metawrap-env/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/kalonjilab/miniconda3/envs/metawrap-env/lib/site_perl/5.26.2 /home/kalonjilab/miniconda3/envs/metawrap-env/lib/5.26.2/x86_64-linux-thread-multi /home/kalonjilab/miniconda3/envs/metawrap-env/lib/5.26.2 .) at /home/kalonjilab/miniconda3/envs/metawrap-env/bin/run_MaxBin.pl line 4. BEGIN failed--compilation aborted at /home/kalonjilab/miniconda3/envs/metawrap-env/bin/run_MaxBin.pl line 4.

----- looks like our default perl libraries are not the conda ones. Manually setting perl5 ----- ----- library directory -----

metawrap path: /home/kalonjilab/miniconda3/envs/metawrap-env/bin/metawrap Will use perl5 libraries located in /home/kalonjilab/miniconda3/envs/metawrap-env/lib/perl5/site_perl/5.22.0 - hopefully they are there. Install Perl in the conda environment if the directory does not exist.

----- Starting binning with MaxBin2... -----

mkdir: cannot create directory ‘KRI_bins//work_files/maxbin2_out’: File exists Can't locate LWP/Simple.pm in @INC (you may need to install the LWP::Simple module) (@INC contains: /home/kalonjilab/miniconda3/envs/metawrap-env/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /home/kalonjilab/miniconda3/envs/metawrap-env/lib/perl5/site_perl/5.22.0 /home/kalonjilab/miniconda3/envs/metawrap-env/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/kalonjilab/miniconda3/envs/metawrap-env/lib/site_perl/5.26.2 /home/kalonjilab/miniconda3/envs/metawrap-env/lib/5.26.2/x86_64-linux-thread-multi /home/kalonjilab/miniconda3/envs/metawrap-env/lib/5.26.2 .) at /home/kalonjilab/miniconda3/envs/metawrap-env/bin/run_MaxBin.pl line 4. BEGIN failed--compilation aborted at /home/kalonjilab/miniconda3/envs/metawrap-env/bin/run_MaxBin.pl line 4.

Something went wrong with running MaxBin2. Exiting.

mojingmj123 commented 1 year ago

I'm having the same issue