[Bioperl-l] RFC: Bio::App::SELEX::RNAmotifAnalysis

[Alexey Morozov]

2012/8/24 Leon Timmermans <l.m.timmermans at students.uu.nl>

> On Thu, Aug 23, 2012 at 12:12 AM, Bottoms, Christopher A
> <BottomsC at missouri.edu> wrote:
> > I developed this application for a research lab here at the University
> of Missouri. I was wondering if this sounded okay and if it were okay to
> use the "Bio" namespace.
>
> That's perfectly fine.
>
> > --------------------------------------
> > SYNOPSIS
> >         perl perl5/lib/perl5/Bio/App/SELEX/RNAmotifAnalysis.pm --infile
> simple.seqs --cpus 4 --run
>
> That is a bit wrong. .pm files are modules, not scripts. You're better
> off adding a small script that uses your module.
>
> > EXAMPLE USE
> >         perl perl5/lib/perl5/Bio/App/SELEX/RNAmotifAnalysis.pm --infile
> simple.seqs --cpus 4 --run
> >
> >         (The file 'simple.seqs' should only contain sequences, one per
> line.)
>
> Why are you not using a proper sequence format, Bio::SeqIO will allow
> you to accept any common format.
>
> >         Install Infernal, MAFFT, and the RNA Vienna package ahead of
> time and add
> >         the directories containing their executables to your PATH, so
> that the
> >         first time you run RNAmotifAnalysis.pm a configuration file
> (cluster.cfg)
> >         will be generated for you with all of the correct parameters.
> Otherwise,
> >         you'll need to update your cluster.cfg file manually.
> >
> >         After installing mafft, Infernal, and Vienna RNA packages, add
> the
> >         directories in which their executables reside in your PATH.
> >
> >         For example, assuming that the mafft executable is located in
> the directory
> >         '/usr/local/myapps/bin/', you would want to add it to your PATH.
>  To make
> >         sure this is done every time you open a terminal window, add
> this to your
> >         .bashrc file, thus:
> >
> >             echo 'export PATH=/usr/local/myapps/bin:$PATH' >> ~/.bashrc.
> >
> >         Then, to make it effective immediately, you can source your
> .bashrc file:
> >
> >             source ~/.bashrc
>
> If possible (perhaps it's not), you may want to create a so called
> Alien package that installs those requirements itself. Not sure if
> that's possible, and probably not that urgent either.
>
> > INSTALLATION
> >             For Debian or Ubuntu systems (tested on Debian 5.06, Ubuntu
> 12-04 LTS)
> >
> >                 Open a terminal and then type the following commands,
> answering
> >                 all questions in the afirmative:
> >
> >                     sudo apt-get install gcc
> >                     sudo apt-get install make
>
> The package you're looking for is called build-essentials
>
> >         (2) Either (a) download and run our installer or (b) use a CPAN
> client
> >             to install Bio::App::SELEX::RNAmotifAnalysis. Note that our
> installer
> >             creates the directory 'perl5' inside your home directory.
> This
> >             directory is for holding Perl modules, including this module
> and any
> >             Perl module dependencies not already included on your
> system. The
> >             installer also appends commands to your .bashrc file to make
> it easy
> >             for the Perl runtime to find these new modules (i.e. it
> includes your
> >             local 'perl5/lib/perl5' directory in the PERL5LIB environment
> >             variable).
> >
> >             (a) Use the installer
> >                   i. Download installer (and name it "installer")
> >
> >                         curl -o installer -L
> http://ircf.rnet.missouri.edu:8000/share.attachment/184
>
> That download doesn't work for me.
>
> >                  ii. Make it executable
> >
> >                         chmod u+x installer
> >
> >                 iii. Run it. In a few cases (e.g. CentOS 5.5) we've had
> to run the
> >                      installer as many as three times to get all of the
> Perl
> >                      modules installed. Please contact us if this
> doesn't work
> >                      after three attempts.
> >
> >                         ./installer
>
> If it has that many issues, it's probably wrong. I'd strongly
> recommend going to CPAN way.
>
> >             (b) If you prefer using a CPAN client, then we recommend
> that you install
> >                 Bio::App::SELEX::RNAmotifAnalyis 'locally' instead of to
> system
> >                 perl, to avoid overwriting core Perl modules. If this
> doesn't make
> >                 sense to you, then please be sure to use the installer as
> >                 described in (a) above.
>
> Installing locally is usually a good idea, I recommend local::lib in
> particular. This «overwriting core Perl modules» suggests to me you're
> doing something wrong anyway though.
>
> Leon
>
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>

So one is free to do whatever he pleases and call it Bio::MyAwesomeStuff,
right? What is required to get to official bioperl distribution? I think
some of my code might eventially prove useful.

Alexey Morozov
LIN SB RAS
Irkutsk, Russia