Perl error when installing program in linux-based server

[ruthbpaula]

I have been trying to install Mfannot in a linux-based server. When I run “mfannot –h” to test the program I keep getting the following error:

Can't locate PirObject.pm in @INC (you may need to install the PirObject module) (@INC contains: /home/pfonseca/Mfannot/mf2sqn/qualifs.pl /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/pfonseca/Mfannot/MFannot/mfannot line 52.
BEGIN failed--compilation aborted at /home/pfonseca/Mfannot/MFannot/mfannot line 52.

It seems to be a problem with the perl version, but I have installed multiple versions and the program still does not recognize it.

Do you have any thoughts about how to fix this so I can successfully run Mfannot in the local server?

I would also like to ask if the webserver is still working (https://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl). Last weekend I have submitted a sequence but still did not get the result.

Thank you in advance,
Ruth

[natacha-beck]

Hi Ruth,

It seems like the installation of the PirObject library was not properly done

You should:

1. Install the PirObject library, you can have a look here.
2. Install the PirModels: https://github.com/BFL-lab/PirModels
3. Setup an environment variable that point to the location of your PirModels for example: ENV PIR_DATAMODEL_PATH /root/PirModels

Hope it will help you to set up properly.

Thanks to bringing to our attention the webserver issue we will have a look.

[natacha-beck]

@ruthbpaula were you able to get the installation done ?

[ruthbpaula]

Hello, Yes, the installation is done; thank you. But we had issues trying to use the --tbl option (no output was being generated). Did you have any similar problems in the past? Best, Ruth Em seg., 28 de dez. de 2020 às 16:49, Natacha Beck <notifications@github.com> escreveu:

…

@ruthbpaula <https://github.com/ruthbpaula> were you able to get the installation done ? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AG5UY6GSJIHJEJQPOE7O32LSXEDQNANCNFSM4VBZWN5A> .

-- *Ruth Barros De Paula* *MSc. student in Genetics and Epigenetics - The University of Texas Health Science Center at Houston - MD Anderson Cancer Center* *BSc. in Biological Sciences - Universidade Federal de Minas Gerais*

[natacha-beck]

Hi Ruth,

I suspect an issue with the installation of the MF2sqn, can you refer to the document and get it a try.
You can run MFannot with the option -d to get more trace and help you to debug.

I wish you all the best for 2021!

[natacha-beck]

@ruthbpaula were you able to get the installation done ?

[tallnuttrbgv]

The PirObject install instructions say to put it in the perl5 lib directory, which I did, but still get this error.