<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37509?offset=10 https://bioinformaticsonline.com/bookmarks/view/26424/biotoolbox Fri, 19 Feb 2016 09:14:44 -0600 https://bioinformaticsonline.com/bookmarks/view/26424/biotoolbox <![CDATA[BioToolbox]]> This is a collection of libraries and high-quality end-user scripts for bioinformatic analysis, including working with gene annotation, collecting data scores from a variety of modern file formats, and conversion between file formats. The Bio::ToolBox libraries provide a unified, abstracted interface to multiple common gene annotation formats and the collection of data from multiple data files. They rely on BioPerl SeqFeature libraries and related adaptors to access binary file formats including Bam, BigWig, BigBed, and USeq. The Bio::ToolBox package includes scripts for setting up databases of annotation, collecting annotated features, collecting genomic data relative to features, manipulating and analyzing data, and data format conversion.

More at http://cpansearch.perl.org/src/TJPARNELL/

Address of the bookmark: http://cpansearch.perl.org/src/TJPARNELL/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30696/many-core-engine-mce-for-perl-example Tue, 31 Jan 2017 05:37:50 -0600 https://bioinformaticsonline.com/bookmarks/view/30696/many-core-engine-mce-for-perl-example <![CDATA[Many-Core Engine (MCE) for Perl example]]> MCE spawns a pool of workers and therefore does not fork a new process per each element of data. Instead, MCE follows a bank queuing model. Imagine the line being the data and bank-tellers the parallel workers. MCE enhances that model by adding the ability to chunk the next n elements from the input stream to the next available worker.

CORE MODULES

Three modules make up the core engine for MCE.

MCE::Core

Provides the Core API for Many-Core Engine. The various MCE options are described here.

MCE::Signal

Temporary directory creation, cleanup, and signal handling.

MCE::Util

Utility functions for Many-Core Engine.

MCE EXTRAS

There are 4 add-on modules for use with MCE.

MCE::Candy

Provides a collection of sugar methods and output iterators for preserving output order.

MCE::Mutex

Provides a simple semaphore implementation supporting threads and processes.

MCE::Queue

Provides a hybrid queuing implementation for MCE supporting normal queues and priority queues from a single module. MCE::Queue exchanges data via the core engine to enable queuing to work for both children (spawned from fork) and threads.

MCE::Relay

Enables workers to receive and pass on information orderly with zero involvement by the manager process while running.

MCE MODELS

The models take Many-Core Engine to a new level for ease of use. Two options (chunk_size and max_workers) are configured automatically as well as spawning and shutdown.

MCE::Loop

Provides a parallel loop utilizing MCE for building creative loops.

MCE::Flow

A parallel flow model for building creative applications. This makes use of user_tasks in MCE. The author has full control when utilizing this model. MCE::Flow is similar to MCE::Loop, but allows for multiple code blocks to run in parallel with a slight change to syntax.

MCE::Grep

Provides a parallel grep implementation similar to the native grep function.

MCE::Map

Provides a parallel map model similar to the native map function.

MCE::Step

Provides a parallel step implementation utilizing MCE::Queue between user tasks. MCE::Step is a spin off from MCE::Flow with a touch of MCE::Stream. This model, introduced in 1.506, allows one to pass data from one sub-task into the next transparently.

MCE::Stream

Provides an efficient parallel implementation for chaining multiple maps and greps together through user_tasks and MCE::Queue. Like with MCE::Flow, MCE::Stream can run multiple code blocks in parallel with a slight change to syntax from MCE::Map and MCE::Grep.

MISCELLANEOUS

Miscellaneous additions included with the distribution.

MCE::Examples

Describes various demonstrations for MCE including a Monte Carlo simulation.

MCE::Subs

Exports functions mapped directly to MCE methods; e.g. mce_wid. The module allows 3 options; :manager, :worker, and :getter.

REQUIREMENTS

Perl 5.8.0 or later. PDL::IO::Storable is required in scripts running PDL.

SOURCE AND FURTHER READING

The source, cookbook, and examples are hosted at GitHub.

SEE ALSO

MCE::Shared provides data sharing capabilities for MCE. It includes MCE::Hobo for running code asynchronously.

Address of the bookmark: https://github.com/marioroy/mce-examples

]]> Jit https://bioinformaticsonline.com/bookmarks/view/33689/bio-graphics-237 Sun, 25 Jun 2017 17:52:21 -0500 https://bioinformaticsonline.com/bookmarks/view/33689/bio-graphics-237 <![CDATA[Bio-Graphics-2.37]]> BioPerl modules Bio::Graphics + Bio::DB:GFF and example scripts. It can draw some of the (but not all) feature types GBrowse can draw. This script should contain everything you can probably make use of (e.g. transcripts, segments, etc.) and you can try to find a good way of visualization by experimenting with its options.

http://search.cpan.org/~lds/Bio-Graphics-2.37/

Address of the bookmark: http://search.cpan.org/~lds/Bio-Graphics-2.37/

]]> Jit https://bioinformaticsonline.com/blog/view/34864/installing-perl-environment-on-linux Tue, 26 Dec 2017 21:21:50 -0600 https://bioinformaticsonline.com/blog/view/34864/installing-perl-environment-on-linux <![CDATA[Installing Perl environment on Linux]]> By using plenv, you can easily install and switch among different version of Perl. This will be installed under your home directory in~/.plenv.

Install latest Perl (with supporting multithreading) and CPANMinus.

 $ cd
 $ git clone git://github.com/tokuhirom/plenv.git ~/.plenv
 $ git clone git://github.com/tokuhirom/Perl-Build.git ~/.plenv/plugins/perl-build/
 $ echo 'export PATH="$HOME/.plenv/bin:$PATH"' >> ~/.bashrc
 $ echo 'eval "$(plenv init -)"' >> ~/.bashrc
 $ source ~/.bashrc
 $ plenv install 5.18.1 -Dusethreads
 $ plenv rehash
 $ plenv global 5.18.1
 $ plenv install-cpanm
  • git is a distributed revision control and source code management software which can help you to download files from GitHub server.
  • echo means "print".
  • >> means adding the output into the end of the file, while > means adding the output by overwriting the whole file. Please use> with additional cares.
  • In Linux system, there are two types of outputs when you execute a command. One is called standard output (or sometimes STDOUT for short), and the other is a standard error (STDERR). 1> is for STDOUT only, 2> is for STDERR only, and &>means for both. In default > is the same to 1>.
  • exec is execution.
  • Remember to install Perl in supporting multithreading (with option -Dusethreads), which is important for many NGS analysis packages (e.g. Trinity). In this setting, you can use multiple CPU for Perl software.
  • Install the CPAN (Comprehensive Perl Archive Network) manager software, CPANMinus, by install-cpanm.

You can use plenv global and plenv local to change the different version of Perl to fulfil different needs of your Perl software.

For example, if the specific version of Perl is not compatible with your script, you can switch to the different version by:

 $ plenv local
  • It is similar to set the local version of your script language when you use pyenv and rbenv as the following.

Put the following path into ~/.bashrc file.

export PERL5LIB="$HOME/.plenv/build/perl-5.18.1/lib"

Install BioPerl and PerlIO::gzip

CPANMinus is a very good Perl module manager, use cpanm to install BioPerl can save you a lot of time. Here are some useful modules:

$ cpanm Bio::Perl
$ cpanm Bio::SearchIO
$ cpanm PerlIO::gzip

For more information, please visit: https://github.com/tokuhirom/plenv

 
]]> biogeek https://bioinformaticsonline.com/bookmarks/view/36927/restrictiondigest-a-powerful-perl-module-for-simulating-genomic-restriction-digests Tue, 12 Jun 2018 13:17:13 -0500 https://bioinformaticsonline.com/bookmarks/view/36927/restrictiondigest-a-powerful-perl-module-for-simulating-genomic-restriction-digests <![CDATA[RestrictionDigest: A powerful Perl module for simulating genomic restriction digests]]> Address of the bookmark: https://github.com/JINPENG-WANG/RestrictionDigest

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38067/metaplotr-a-perlr-pipeline-for-plotting-metagenes-of-nucleotide-modifications-and-other-transcriptomic-sites Mon, 05 Nov 2018 08:12:45 -0600 https://bioinformaticsonline.com/bookmarks/view/38067/metaplotr-a-perlr-pipeline-for-plotting-metagenes-of-nucleotide-modifications-and-other-transcriptomic-sites <![CDATA[MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites]]> An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Address of the bookmark: https://github.com/olarerin/metaPlotR

]]> Neel https://bioinformaticsonline.com/opportunity/view/41043/postdoctoral-scientist-genome-analytics-genome-bioinformatics-mf Sun, 16 Feb 2020 02:57:40 -0600 <![CDATA[Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)]]> https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html
Your profile:
Degree in bioinformatics, biostatistics, or equivalent
Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing
Strong competence in working in Unix/Linux environments (shell)
Strong programming skills (in particular: Python, R, Perl)
Experience with using git and snakemake
Fluent English language skills, both spoken and written
Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team

Additional Information:

If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.

]]> https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 Fri, 07 Jul 2017 04:06:59 -0500 https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 <![CDATA[Awesome perl frameworks, libraries and software - PART 1]]> A curated list of awesome Perl frameworks, libraries and software.

]]> Neel https://bioinformaticsonline.com/bookmarks/view/33866/perlbrew-admin-free-perl-installation-management-tool Wed, 12 Jul 2017 03:53:08 -0500 https://bioinformaticsonline.com/bookmarks/view/33866/perlbrew-admin-free-perl-installation-management-tool <![CDATA[Perlbrew: admin-free perl installation management tool.]]> perlbrew is an admin-free perl installation management tool. The latest version is 0.79, read the release note: Release 0.79. 

Copy & Paste this line into your terminal:

\curl -L https://install.perlbrew.pl | bash

Or, if your system does not have curl but something else:

# Linux
\wget -O - https://install.perlbrew.pl | bash

# FreeBSD
\fetch -o- https://install.perlbrew.pl | sh

If you prefer to install with cpan, there are two steps:

sudo cpan App::perlbrew
perlbrew init

If it is installed with cpan, the perlbrew executable should be installed as /usr/bin/perlbrew or /usr/local/bin/perlbrew. For all users who want to use perlbrew, a prior perlbrew init needs to be executed.

The default perlbrew root directory is ~/perl5/perlbrew, which can be changed by setting PERLBREW_ROOTenvironment variable before the installation and initialization. For more advanced installation process, please read the perlbrew document.

 

Address of the bookmark: https://perlbrew.pl/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39913/twinblast-when-two-is-better-than-one Sat, 07 Sep 2019 08:50:08 -0500 https://bioinformaticsonline.com/bookmarks/view/39913/twinblast-when-two-is-better-than-one <![CDATA[TwinBLAST: When Two Is Better than One]]> TwinBLAST is a web-based tool for viewing 2 BLAST reports simultaneouslyside-by-side. It uses ExtJS (www.sencha.com/products/extjs/) to provide 2independently scrollable panels. BioPerl (www.bioperl.org) is used to indexraw BLAST reports and Bio::Graphics is used to draw pictograms of the BLASThits.

https://github.com/IGS/twinblast

https://mra.asm.org/content/8/35/e00842-19

Address of the bookmark: https://github.com/IGS/twinblast

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