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Tony: Do you need 1.7 for some specific reason? It may be better to go with bcl2fastq (v.1.8.4) otherwise.
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Sorry, this is bcl2fastq 1.8.4. Thought it easier to post to the same thread as CASSAVA as bcl2fastq is/was part of CASSAVAOriginally posted by GenoMax View PostComment
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Can you try installing the rpm package (http://namhuy.net/1207/how-to-instal...-debian.html)? That may be simpler.Comment
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I tried that. I could get the deb created but installing fails with no errors after unpacking.Originally posted by GenoMax View Post
I should add that Setting up bcl2fastq lasts about 3 seconds before exiting. configureBclTofastq.pl goes into my path, but returns errors when I try and run it.Code:admin@seq-analysis:~/bcl$ sudo alien bcl2fastq-1.8.4-Linux-x86_64.rpm bcl2fastq_1.8.4-2_amd64.deb generated admin@seq-analysis:~/bcl$ sudo dpkg -i bcl2fastq_1.8.4-2_amd64.deb (Reading database ... 273160 files and directories currently installed.) Preparing to unpack bcl2fastq_1.8.4-2_amd64.deb ... Unpacking bcl2fastq (1.8.4-2) over (1.8.4-2) ... Setting up bcl2fastq (1.8.4-2) ... admin@seq-analysis:~/bcl
Code:configureBclTofastq.pl --input-dir ./140321_M01520_0085_000000000-A7FD0/Data/Intensities/BaseCalls/ "my" variable $value masks earlier declaration in same statement at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 760. syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 747, near "$variable qw(ELAND_FASTQ_FILES_PER_PROCESS)" Global symbol "$variable" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 749. syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 751, near "$directory qw(ELAND_GENOME)" Global symbol "$self" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753. Global symbol "$directory" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753. Global symbol "$project" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753. Global symbol "$sample" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753. Global symbol "$lane" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753. Global symbol "$barcode" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753. Global symbol "$reference" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753. syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 761, near "}" /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm has too many errors. Compilation failed in require at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61. BEGIN failed--compilation aborted at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61. Compilation failed in require at /usr/local/bin/configureBclToFastq.pl line 250. BEGIN failed--compilation aborted at /usr/local/bin/configureBclToFastq.pl line 250.
Last edited by TonyBrooks; 05-01-2014, 07:19 AM.Comment
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Tony: You need to minimally provide a samplesheet by specifying --samplesheet Samphesheet_file.csv (it needs to be in a specific format). I have an example in this post: http://seqanswers.com/forums/showpos...4&postcount=14
Can you try this?
--fastq-cluster-count makes a single gz file for a sample. If you do not want that then remove that option.Code:$ configureBclTofastq.pl --input-dir ./140321_M01520_0085_000000000-A7FD0/Data/Intensities/BaseCalls/ --samplesheet /path_to/samplesheet.csv --fastq-cluster-count 0
Last edited by GenoMax; 05-01-2014, 08:00 AM.Comment
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Same problemOriginally posted by GenoMax View Post
I think I may have found the problem. I'm wondering if the problem is to do with the version of boost installed. I'm going to try and remove and install an older version and see if it worksComment
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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.Comment
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Yes it is. I'm sorry for submitting without a quoting.Originally posted by GenoMax View Post
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.Comment
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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?Comment
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Thnak you GenoMax for asking me further information.Originally posted by GenoMax View Post
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.Comment
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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.Comment
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Ubuntu 13.10 : perl v5.14.2-21Originally posted by GenoMax View Post
Ubuntu 14.04 LTS : perl v5.18.2-2
So far, I have used only system default perls.Comment
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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.Comment
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BINGO! GenoMax, I appreciate your informative advices.Originally posted by GenoMax View Post
The followings are a protocol to prepare to use Bcl2Fastq on Ubuntu 14.04 LTE:
note: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
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.Comment
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