COMMON.pm module

[DL Wu]

Hi, Everyone,

I am trying to run Trinity on a cloud instance. It gave me this error:

Can't locate COMMON.pm in @INC (you may need to install the COMMON module) (@INC contains: /usr/local/bin/PerlLib /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/bin/Trinity line 14.
BEGIN failed--compilation aborted at /usr/local/bin/Trinity line 14.

I could not find any COMMON module at perl CPAN site.

Any suggestions?
Dongliang

[Brian Haas]

The Trinity script has to stay positioned in the context of the Trinity software package.  You can move the entire package into /usr/local/bin, but you can't relocate the Trinity scritpt alone.

best,

~brian

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[DL Wu]

The folder trinityrnaseq-2.0.6 is in /usr/local/bin as well as the Trinity command file.
Do you mean I should copy all of the files inside trinityrnaseq-2.0.6 to the /usr/local/bin folder?
There is also a Trinity file inside the trinityrnaseq-2.0.6 folder. Please clarify

Thanks,
Dongliang

On Thursday, March 19, 2015 at 1:48:41 PM UTC-10, Brian Haas wrote:

The Trinity script has to stay positioned in the context of the Trinity software package.  You can move the entire package into /usr/local/bin, but you can't relocate the Trinity scritpt alone.

best,

~brian

On Thu, Mar 19, 2015 at 6:29 PM, DL Wu <dragont...@gmail.com> wrote:

Hi, Everyone,

I am trying to run Trinity on a cloud instance. It gave me this error:

Can't locate COMMON.pm in @INC (you may need to install the COMMON module) (@INC contains: /usr/local/bin/PerlLib /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/bin/Trinity line 14.
BEGIN failed--compilation aborted at /usr/local/bin/Trinity line 14.

I could not find any COMMON module at perl CPAN site.

Any suggestions?
Dongliang

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[Brian Haas]

You would run trinity as

 /usr/local/bin/trinityrnaseq-2.0.6/Trinity

best,

~brian

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[Brian Haas]

Hi Dongliang,

I can't think of why it would be looking for read files within the trinity folder, unless you were trying to run the sample data set through via the incluided runMe script.

best,

~b

On Thu, Mar 19, 2015 at 10:56 PM, DL Wu <dragont...@gmail.com> wrote:

Thanks, It works, but when I tried to run the reads in my home folder. It was looking for the files in the trinityrnseq-2.0.6 folder.
I remember it ran OK with my read files in my home folder in another instance. Any insight?

Best,
Dongliang

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[DL Wu]

Sorry, I made typo for my input files. That's why trinity can not find them.
Thanks for your response.
Dongliang