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sadaf #154

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Safmughal opened this issue Jun 22, 2015 · 7 comments
Closed

sadaf #154

Safmughal opened this issue Jun 22, 2015 · 7 comments

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@Safmughal
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Hi. I downloaded Roary on our iridis (SSH). I am having a problem while trying to run (roary *.gff) on command line. The error looks something like that

EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open PROKKA_SG1.gff.proteome.faa.intermediate.extracted.fa: No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /local/software/perl-modules/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::Root::IO::_initialize_io /local/software/perl-modules/share/perl5/Bio/Root/IO.pm:351
STACK: Bio::SeqIO::_initialize /local/software/perl-modules/share/perl5/Bio/SeqIO.pm:491
STACK: Bio::SeqIO::fasta::_initialize /local/software/perl-modules/share/perl5/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /local/software/perl-modules/share/perl5/Bio/SeqIO.pm:372
STACK: Bio::SeqIO::new /local/software/perl-modules/share/perl5/Bio/SeqIO.pm:413
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/ExtractProteomeFromGFF.pm:138
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/ExtractProteomeFromGFF.pm:152
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/ExtractProteomeFromGFF.pm:43
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:79

STACK: /local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/bin/extract_proteome_from_gff:18
@Safmughal Safmughal reopened this Jun 22, 2015
@andrewjpage
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Hi,
What operating system are you running? If its an older version of Linux or
a more obscure version, you'll need to install the dependancies through
your package management system yourself, or install them from source. For
example on CentOS/RedHat, this requires adding extra bioinformatics
repositories so that RPMs are available. The ./install_dependancies.sh
script may also work for you.
Regards,
Andrew

On 22 June 2015 at 10:08, Safmughal notifications@github.com wrote:

Hi. I downloaded Roary on our iridis (SSH). I am having a problem while
trying to run (roary *.gff) on command line. The error looks something like
that

EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open PROKKA_SG1.gff.proteome.faa.intermediate.extracted.fa:
No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw
/local/software/perl-modules/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::Root::IO::_initialize_io
/local/software/perl-modules/share/perl5/Bio/Root/IO.pm:351
STACK: Bio::SeqIO::_initialize
/local/software/perl-modules/share/perl5/Bio/SeqIO.pm:491
STACK: Bio::SeqIO::fasta::_initialize
/local/software/perl-modules/share/perl5/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new
/local/software/perl-modules/share/perl5/Bio/SeqIO.pm:372
STACK: Bio::SeqIO::new
/local/software/perl-modules/share/perl5/Bio/SeqIO.pm:413
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate
/local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/ExtractProteomeFromGFF.pm:138
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein
/local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/ExtractProteomeFromGFF.pm:152
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file
/local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/ExtractProteomeFromGFF.pm:43
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run
/local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:79
STACK:
/local/software/roary/3.0.3/source/sanger-pathogens-Roary-5685c8b/bin/extract_proteome_from_gff:18

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#154.

@Safmughal
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Hi,
Thanks for your quick response. In response to your above comments, I have the following information.
The operating system is quite an old version of RedHat, RHEL v6.3. To do the installation I modified install_dependencies.sh by taking out all the Ubuntu commands/features, and then executed that script. This built copies of Parallel, Bedtools, Cd-hit and Prank in the build directory.
The installation of the perl modules was a bit more complicated. Initially, I installed the modules as listed in install_dependencies.sh, however subsequently I had to install a lot more modules. I decided to repeatedly run one of the roary scripts until there where no longer any perl related errors. The final list of perl modules is here:

parent, Graph::Writer::Dot, Sub::Exporter, Eval::Closure, Devel::OverloadInfo, Package::DeprecationManager, B::Hooks::EndOfScope, Package::Stash, namespace::clean, Module::Implementation, Data::OptList, Class::Load, Moose, Moose::Role, Test::Files, Graph::Writer, File::Which, Log::Log4perl, Text::CSV, Graph, File::Slurp::Tiny, File::Grep, File::Find::Rule, Exception::Class, Array::Utils

Some of the perl modules had to forcibly installed due to test errors. My final observation is that there doesn't appear to be a "BEDTOOLS_LIB_DIR", however I'm not sure why.

I hope the above details help.
Kind Regards
Sadaf

@andrewjpage
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Hi Sadaf,
I've just pushed up a newer version of the install script and some install
instructions for CentOS/Redhat. It might help somewhat and it builds all of
the external dependancies (and the ubuntu commands have been excluded).
I'm afraid I dont normally work with this distribution, so I'm working of a
basic centos6 vagrant box, so please excuse the not so neat instructions.
Alternatively you can use LinuxBrew http://brew.sh/linuxbrew/

With regards to the perl modules, 'cpanm Bio::Roary' should install all the
missing dependancies automatically.

Thanks for the feedback.
Andrew

On 22 June 2015 at 11:36, Safmughal notifications@github.com wrote:

Hi,
Thanks for your quick response. In response to your above comments, I have
the following information.
The operating system is quite an old version of RedHat, RHEL v6.3. To do
the installation I modified install_dependencies.sh by taking out all the
Ubuntu commands/features, and then executed that script. This built copies
of Parallel, Bedtools, Cd-hit and Prank in the build directory.
The installation of the perl modules was a bit more complicated.
Initially, I installed the modules as listed in install_dependencies.sh,
however subsequently I had to install a lot more modules. I decided to
repeatedly run one of the roary scripts until there where no longer any
perl related errors. The final list of perl modules is here:

parent, Graph::Writer::Dot, Sub::Exporter, Eval::Closure,
Devel::OverloadInfo, Package::DeprecationManager, B::Hooks::EndOfScope,
Package::Stash, namespace::clean, Module::Implementation, Data::OptList,
Class::Load, Moose, Moose::Role, Test::Files, Graph::Writer, File::Which,
Log::Log4perl, Text::CSV, Graph, File::Slurp::Tiny, File::Grep,
File::Find::Rule, Exception::Class, Array::Utils

Some of the perl modules had to forcibly installed due to test errors. My
final observation is that there doesn't appear to be a "BEDTOOLS_LIB_DIR",
however I'm not sure why.

I hope the above details help.
Kind Regards
Sadaf

—
Reply to this email directly or view it on GitHub
#154 (comment)
.

@andrewjpage
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Member

Hi Sadaf,
Doing a bit more playing around on CentOS6.6, it seems LinuxBrew is the
most straightforward way of setting up the software and installing the
dependancies.
So follow the instructions for Fedora here http://brew.sh/linuxbrew/
then:

brew tap homebrew/science

brew install bedtools cd-hit blast mcl prank parallel mafft exonerate
fasttree

cpanm -f Bio::Roary

Regards,

Andrew

On 22 June 2015 at 13:13, Andrew Page andrewjpage@gmail.com wrote:

Hi Sadaf,
I've just pushed up a newer version of the install script and some install
instructions for CentOS/Redhat. It might help somewhat and it builds all of
the external dependancies (and the ubuntu commands have been excluded).
I'm afraid I dont normally work with this distribution, so I'm working of a
basic centos6 vagrant box, so please excuse the not so neat instructions.
Alternatively you can use LinuxBrew http://brew.sh/linuxbrew/

With regards to the perl modules, 'cpanm Bio::Roary' should install all
the missing dependancies automatically.

Thanks for the feedback.
Andrew

On 22 June 2015 at 11:36, Safmughal notifications@github.com wrote:

Hi,
Thanks for your quick response. In response to your above comments, I
have the following information.
The operating system is quite an old version of RedHat, RHEL v6.3. To do
the installation I modified install_dependencies.sh by taking out all the
Ubuntu commands/features, and then executed that script. This built copies
of Parallel, Bedtools, Cd-hit and Prank in the build directory.
The installation of the perl modules was a bit more complicated.
Initially, I installed the modules as listed in install_dependencies.sh,
however subsequently I had to install a lot more modules. I decided to
repeatedly run one of the roary scripts until there where no longer any
perl related errors. The final list of perl modules is here:

parent, Graph::Writer::Dot, Sub::Exporter, Eval::Closure,
Devel::OverloadInfo, Package::DeprecationManager, B::Hooks::EndOfScope,
Package::Stash, namespace::clean, Module::Implementation, Data::OptList,
Class::Load, Moose, Moose::Role, Test::Files, Graph::Writer, File::Which,
Log::Log4perl, Text::CSV, Graph, File::Slurp::Tiny, File::Grep,
File::Find::Rule, Exception::Class, Array::Utils

Some of the perl modules had to forcibly installed due to test errors. My
final observation is that there doesn't appear to be a "BEDTOOLS_LIB_DIR",
however I'm not sure why.

I hope the above details help.
Kind Regards
Sadaf

—
Reply to this email directly or view it on GitHub
#154 (comment)
.

@Safmughal
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Author

Thanks Andrew for your efforts. I appreciate that. I will update you once I will go through it.
Kind Regards
Sadaf

@Safmughal
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Author

Hi Andrew,
Just to let you know that the roary is working perfectly fine on our system. Thanks for your immense support and efforts to resolve the installation issue.

Kind Regards
Sadaf

@andrewjpage
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Member

Thanks for letting me know.
Andrew

On 23 June 2015 at 09:36, Safmughal notifications@github.com wrote:

Hi Andrew,
Just to let you know that the roary is working perfectly fine on our
system. Thanks for your immense support and efforts to resolve the
installation issue.

Kind Regards
Sadaf

—
Reply to this email directly or view it on GitHub
#154 (comment)
.

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@andrewjpage @Safmughal