YAML/Tiny.pm preventing set-up

[abbyhudak]

When trying to run orthomcl-pipeline-setup.pl, the error message says: Can't locate YAML/Tiny.pm in @INC (you may need to install the YAML::Tiny module). When I try to install this module it fails at installing another module, Devel::Leak::Module and therefore cannot get get the YAML: Tiny module to install.

[apetkau]

Which version of Perl are you running perl --version? Was there any other error messages that were reported? Often when a module fails to install there will be a message along the lines of "More information found in /home/aaron/.cpanm/work/1523283335.5808/build.log".

[abbyhudak]

I am using perl5. I am not getting an error like the one you used as an example. It just says @INC contains: and the pathways. I am not sure why only this one module is having issues. Do you know if there is something on my end I can do to modify the INC so it can find the module?

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From: Aaron Petkau notifications@github.com Sent: Monday, April 9, 2018 7:20:09 AM To: apetkau/orthomcl-pipeline Cc: abbyhudak; Author Subject: Re: [apetkau/orthomcl-pipeline] YAML/Tiny.pm preventing set-up (#16)

Which version of Perl are you running perl --version? Was there any other error messages that were reported? Often when a module fails to install there will be a message along the lines of "More information found in /home/aaron/.cpanm/work/1523283335.5808/build.log".

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/apetkau/orthomcl-pipeline/issues/16#issuecomment-379768743, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AkDxFarv2HHaDhKTDlKX4BKbt9-o-V7Uks5tm24ZgaJpZM4TLydT.

[apetkau]

Well, if the module fails to install then it may not work correctly even if you do add a path to @INC. You could try to install with cpanm --force YAML::Tiny though to force install even when something failed.

Another option is to use a conda environment to install and manage a separate version of Perl and all modules.

You can do this by first downloading and installing conda (https://conda.io/miniconda.html) then running

conda create --name orthomcl -c defaults -c conda-forge -c bioconda perl perl-app-cpanminus

Then, to work with the orthomcl environment and attempt to install YAML::Tiny you could run:

source activate orthomcl
cpanm YAML::Tiny

More information on conda and conda environments can be found at https://conda.io/docs/user-guide/getting-started.html#managing-environments. Also, you may want to check out bioconda for many conda packages related to bioinformatics.

[apetkau]

I am closing this issue. If this is still a problem you may re-open it.

[dtx282000]

Hi, I have faced the same question. the error is as follows: Can't locate YAML/Tiny.pm in @INC (you may need to install the YAML::Tiny module) (@INC contains: /home/dengtx/software/mirdeep2/lib/perl5/x86_64-linux-gnu-thread-multi /home/dengtx/software/mirdeep2/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/x86_64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at scripts/orthomcl-pipeline-setup.pl line 6. BEGIN failed--compilation aborted at scripts/orthomcl-pipeline-setup.pl line 6.

Actually, I have successfully installed the YAML::Tiny module with the command line of cpanm --force YAML::Tiny. Now, I have no idea how to deal with it.

[amymariecampbell]

@dtx282000 Did you ever find a solution to this?