Doubt - installing LncTar software

Question

[kousi31]

Hi all,

I want to install LncTar software.
I have downloaded LncTar as compressed file.
I extracted the folder. The folder has
LncTar.pl file and Genecare folder

Inside the Genecare folder there is a file named - PerlOligos.pm

when I run the command perl LncTar.pl -p 1 - l Examp1_RNA1.txt -m Examp1_RNA2.txt -d -0.1 -s F -o out.txt I get the error

Can't locate Genecare/PerlOligos.pm in @INC (you may need to install the Genecare::PerlOligos module) (@INC contains: /etc/perl /.....

I don't know how to install Genecare. I am a beginner with no knowledge on perl. Help me install LncTar

[Saurav]

Since "genecare" is a custom module/package. You need to add it from LncTar extracted folder to your Perl library.
You need to follow these steps (This is for windows. I think it should also work on Mac/Linux) :

1. Copy "genecare" folder from LncTar extracted folders.
2. Go to c drive where your Perl is installed (The location can vary depending upon where you installed it during the installation process).
3. Go inside "Perl64" and look for the "lib" folder (which is short for "Perl-library" where all the Perl modules are stored).
4. Paste your copied, "Genecare" folder here.
5. Re-run your code: perl LncTar.pl -p 1 - l Examp1_RNA1.txt -m Examp1_RNA2.txt -d -0.1 -s F -o out.txt.

[Lepomis_8]

This partially worked for me! I got an output with the following:

lncRNA is :BC200, length : 200  mRNA is : ARC,  length :2948 
Negative repeat count does nothing at C:/Perl64/lib/Genecare/PerlOligos.pm line 556, <MRNA_FILE> line 2.

The out.txt file is as follows:

Query        Length_Query        Target      Length_Target       dG      ndG         Start_Position_Query        End_Position_Query      Start_Position_Target       End_Position_Target
BC200    200    ARC  2948   -27.57   -0.1421    1   200 59  258

I don't think this is the full result. Any ideas? I've tried contacting the developers but got no response.

[Jeremiah]

It is the full result, there is only one lncRNA and one mRNA in Examp1, and the output file is just like web version reult

[ATpoint]

This is a pure Perl issue: http://www.cpan.org/modules/INSTALL.html

[kousi31]

I tried cpan App::cpanminus
then sudo cpanm Genecare::PerlOligos

Got error

Finding Genecare::PerlOligos on cpanmetadb failed. ! Finding Genecare::PerlOligos () on mirror http://www.cpan.org failed. ! Couldn't find module or a distribution Genecare::PerlOligos

The link says cpanm Module::Name in this what is the Module and Name?

[ATpoint]

Ok, seems to be a custom module which is not published in cpan. I got a different error:

perl LncTar.pl -p 1 -l Examp1_RNA1.txt -m Examp1_RNA2.txt -d -0.1 -s F -o out.txt
lncRNA is :BC200, length : 200  mRNA is : ARC,  length :2948
Negative repeat count does nothing at Genecare/PerlOligos.pm line 556, <MRNA_FILE> line 2.

It even started with the fact that the downloaded archive was named LncTar.rar instead of .tar

Maybe try emailing the authors or use the web version.

[kousi31]

Thank you for your suggestions.

[youyi]

I have the same issue.

Negative repeat count does nothing...

There any solution for this issue?

Thanks

[ustcxijing]

Hi kousi31,

I'm having the same issue. I sent an email to the authors several days ago, but haven't got reply yet. Have you fixed the issue? If so, please let me know. I need to use the software now.

Also, I want to ask whether someone has experiences on using the web version. If I want to run some non-coding RNAs against a whole transcriptome, how can I input the transcriptome on the web version? Thanks!

[ATpoint]

I am not a perl guy so cannot really comment but maybe you should explore the source code and see if it expects a specific version of either perl itself or of some common dependencies. I mean the tool must work for the developers, they probably and simply missed to put all necessary steps into the manual to make it run.

[ustcxijing]

Thanks for your comments, ATpoint. I plan to try web version first to see whether it works.

[Ram]

Please do not add an answer unless you're answering the top level question.

Answer 1

[h.mon]

Perl searches modules using the paths stored in the array @INC. Paths stored in the environment variable PERL5LIB are added to @INC, so you need to add the directory where you installed LncTar to the environment variable PERL5LIB:

export PERL5LIB=/path/to/LncTar:$PERL5LIB
perl /path/to/LncTar/LncTar.pl

param error ,please check out and run again
Usage: perl LncTar.pl [-p kind] [-l lncfile] [-m mrnafile] [-d delta] [-s WhetherPic ] [-o outfile] 
Usage: perl LncTar.pl [-p kind] [-f filename] [-d delta] [-s WhetherPic]  [-o outfile]
  

Alternatively, you can use the -I /path/to/folder/ (capital i) to add a given folder to @INC at run time.