StevenWingett / FastQ-Screen

Detecting contamination in NGS data and multi-species analysis
https://stevenwingett.github.io/FastQ-Screen/
GNU General Public License v3.0
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Fail to install GD module #53

Closed ericjuo closed 2 years ago

ericjuo commented 2 years ago

I follow the installation guide to install prerequisite GD module, but it gives errors:

$ perl -MCPAN -e "install GD"
Reading '/home/ericjuo/.cpan/Metadata'
  Database was generated on Sat, 19 Mar 2022 01:55:59 GMT
Running install for module 'GD'
Checksum for /home/ericjuo/.cpan/sources/authors/id/R/RU/RURBAN/GD-2.76.tar.gz ok
'YAML' not installed, will not store persistent state
Configuring R/RU/RURBAN/GD-2.76.tar.gz with Makefile.PL
Package gdlib was not found in the pkg-config search path.
Perhaps you should add the directory containing `gdlib.pc'
to the PKG_CONFIG_PATH environment variable
No package 'gdlib' found
 at Makefile.PL line 530.
*** can not find package gdlib
*** check that it is properly installed and available in PKG_CONFIG_PATH
 at Makefile.PL line 530.
Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site]
  RURBAN/GD-2.76.tar.gz
  /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK

I am using Ubuntu 20.04.4 LTS

StevenWingett commented 2 years ago

Hi,

Sorry to learn you are experiencing problems with FastQ Screen.

Firstly, if I remember correctly, making plots with GD graph is not essential for FastQ Screen to run. Try running the software on the test dataset. You will probably get a warning message about making PNG plots. However, the output text file and HTML files should still be generated. Is that correct?

If you do want the plots as well, I think you need to install extra libraries to Ubuntu. I did a quick Google search. Maybe this will solve the problem: https://comery.github.io/2018/08/15/An-error-when-install-perl-module-GD/

I hope that helps.

All the best, Steven