Error running ./runMe.sh : Can't locate Data/Dumper.pm in @INC

Ava Hoffman

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Jun 28, 2018, 1:46:35 AM6/28/18

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Hello all,

I am working on getting Trinity set up on a new server and am encountering the following when running ./runMe.sh :

#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G \
              --left reads.left.fq.gz \
              --right reads.right.fq.gz \
              --SS_lib_type RF \
              --CPU 4
Can't locate Data/Dumper.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ../../Trinity line 19.
BEGIN failed--compilation aborted at ../../Trinity line 19.

I'm not really clear on what Dumper.pm does, but I've tried installing it from here : http://www.cpan.org/modules/by-module/Data/Data-Dumper-2.161.tar.gz . The packages seems to make and install successfully but I'm still getting this error.

Any thoughts are much appreciated!

Brian Haas

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Jun 28, 2018, 4:13:52 AM6/28/18

to Ava Hoffman, trinityrnaseq-users

Hi Ava,

This is one of those modules that usually comes standard w/ perl installations, I'm pretty sure.

If it's being installed in one of the perl lib paths:

/usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5

and it's not loading, then I'm not sure... you could try installing a new version of perl and see if that helps. Just be sure that if you run

which perl

that it returns the path to the installation you want to use, and if not, adjust your PATH setting.

best,

~brian

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Brian J. Haas
The Broad Institute
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Ava Hoffman

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Jun 28, 2018, 3:27:03 PM6/28/18

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Installing a local version of perl (5.24) and modifying the PATH seemed to do the trick.

Thanks!

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Brian Haas

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Jun 28, 2018, 4:39:13 PM6/28/18

to Ava Hoffman, trinityrnaseq-users

terrific!

all the best,

~b

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The Broad Institute
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