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Old 05-21-2014, 10:39 AM   #21
HiroMishima
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I have same problem. The rpm file worked on Ubuntu 13.10 using Perl v5.14.2-21, however, it does not work on Ubuntu 14.04 LTS using Perl v5.18.2-2. So far I cannot solve the problem.
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Old 05-21-2014, 11:14 AM   #22
GenoMax
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Quote:
Originally Posted by HiroMishima View Post
I have same problem. The rpm file worked on Ubuntu 13.10 using Perl v5.14.2-21, however, it does not work on Ubuntu 14.04 LTS using Perl v5.18.2-2. So far I cannot solve the problem.
Is this Bcl2fastq install?
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Old 05-21-2014, 04:28 PM   #23
HiroMishima
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Quote:
Originally Posted by GenoMax View Post
Is this Bcl2fastq install?
Yes it is. I'm sorry for submitting without a quoting.

I installed bcl2fastq-1.8.4-Linux-x86_64.rpm using the alien command into Ubuntu 13.10. After upgrading Ubuntu to 14.04 LTS, configureBclToFastq.pl raises errors in Config.pm. These errors are the same as TonyBrooks' post http://seqanswers.com/forums/showpos...9&postcount=18.
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Old 05-22-2014, 04:16 AM   #24
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Have you already tried to reinstall Bcl2fastq after the upgrade to 14.04 using the same method you used as before?

Are you using a valid SampleSheet.csv file?
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Old 05-22-2014, 04:48 PM   #25
HiroMishima
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Quote:
Originally Posted by GenoMax View Post
Have you already tried to reinstall Bcl2fastq after the upgrade to 14.04 using the same method you used as before?

Are you using a valid SampleSheet.csv file?
Thnak you GenoMax for asking me further information.

Before installing bcl2fastq, I purged the package using "sudo dpkg --purge bcl2fastq" to uninstall completely. Errors were not reported during the uninstall process.

I used a SampleSheet.csv file validated on other CentOS machine that can run configureBclToFastq.pl.

On the CentOS machine, "configureBclToFastq.pl --help" returns help messages, however on the Ubuntu14.04 machine, the same command-line returns Perl's errors.
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Old 05-22-2014, 05:37 PM   #26
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Which version of perl do you have as system default on Ubuntu 14.04?

On RHEL we are explicitly using perl 5.12.0 (even though the system perl is set to v.5.8.8) for bcl2fastq.
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Old 05-22-2014, 06:06 PM   #27
HiroMishima
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Quote:
Originally Posted by GenoMax View Post
Which version of perl do you have as system default on Ubuntu 14.04?

On RHEL we are explicitly using perl 5.12.0 (even though the system perl is set to v.5.8.8) for bcl2fastq.
Ubuntu 13.10 : perl v5.14.2-21
Ubuntu 14.04 LTS : perl v5.18.2-2

So far, I have used only system default perls.
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Old 05-22-2014, 06:22 PM   #28
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That could be the potential problem. Newer versions of perl may be more strict on syntax checking which is leading to those errors.

Since you probably do not want to mess with system perl you may want to try something like this to use an older version of perl: http://perlbrew.pl/ I have not tried this myself.
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Old 05-22-2014, 08:14 PM   #29
HiroMishima
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Quote:
Originally Posted by GenoMax View Post
That could be the potential problem. Newer versions of perl may be more strict on syntax checking which is leading to those errors.

Since you probably do not want to mess with system perl you may want to try something like this to use an older version of perl: http://perlbrew.pl/ I have not tried this myself.
BINGO! GenoMax, I appreciate your informative advices.

The followings are a protocol to prepare to use Bcl2Fastq on Ubuntu 14.04 LTE:

Code:
sudo alien -i bcl2fastq-1.8.4-Linux-x86_64.rpm
sudo apt-get install build-essential
curl -kL http://install.perlbrew.pl | bash
echo >> ~/.bash_profile "source ~/perl5/perlbrew/etc/bashrc"
perlbrew install perl-5.14.4
perlbrew switch perl-5.14.4
perlbrew install-cpanm
cpanm XML/Simple.pm
note:
Run as a non-root user.
Installing (build) process took about 10min for my environment.
You can also use "aptitude" instead of "apt-get".
For perlbrew, you can use "use" instead of "switch" to set-up only for current shell.
You may need to install other required modules using cpanm.
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Old 05-23-2014, 03:58 AM   #30
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Excellent! Thank you for documenting the installation steps.
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