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

[Leon Timmermans]

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