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

Christopher Bottoms bottomsc at missouri.edu
Thu Sep 6 18:34:17 EDT 2012


Dear BioPerl Community,

I welcome further comments on Bio::App::SELEX::RNAmotifAnalysis. Below
this message is my updated "perldoc" for it.

A special thanks to Leon Timmermans and Chris Fields for their prior feedback.

Leon, I made several Improvements based on your feedback. Now, a
wrapper script is used instead of the module file itself. FASTQ files
are an acceptable input format. And the installer was improved. I
found that installing Module::Build before our module cleared up
issues with several dependencies. I think that our instructions for
using cpanminus effectively give the same results as using local::lib.
 As for Alien packages, I would really like to work on them, but the
time (i.e. funding) is currently too limited.

Chris,  Yes, the "App" part of the proposed name was chosen because
this is designed more to be an application than to be modules to be
reused. I fully intend to support this distribution myself. If you
think it better to separate it more from the BioPerl namespace, I have
considered using calling it App::Bio::SELEX::RNAmotifAnalysis. What do
you think?

I welcome additional feedback.

Thanks,
Christopher Bottoms


Perldoc for Bio::App::SELEX::RNAmotifAnalysis:


SYNOPSIS
        RNAmotifAnalysis --fastq seqs.fq --cpus 4 --run

DESCRIPTION
        This module pipelines steps in the analysis of SELEX
(Systematic Evolution
        of Ligands through EXponential enrichment) data.

        This main module creates scripts to do the following:

        (1) Cluster similar sequences based on edit distance.

        (2) Align sequences within each cluster (using mafft).

        (3) Calculate the secondary structure of the aligned sequences (using
            RNAalifold, from the Vienna RNA package)

        (4) Build covariance models using cmbuild from Infernal.

        Another useful utility installed with this distribution is
        "selex_covarianceSearch" for doing iterative refinements of
        covariance models.

        If you want to use files that simply list sequences, then use
        the "--simple" flag instead of the "--fastq" flag.

        This script assumes that you've already done all of the quality
        control of your sequences beforehand. If the FASTQ format is
        used, quality scores are ignored.

EXAMPLE USE
        RNAmotifAnalysis --infile seqs.fq --cpus 4 --run

        This will cluster the sequences found in 'seqs.fq' and create
a FASTA file
        for each one. The FASTA files will be grouped into batches (i.e. one per
        cpu requested) that will be placed in a separate directory for
each batch,
        and processed within that directory. At the end of processing, for each
        cluster there will be a covariance model and postscript illustration
        files. The batch script used to process each batch will be
located in the
        respective batch directory.  To produce the scripts without
running them,
        simply exclude the --run flag from the command line.

CONFIGURATION AND ENVIRONMENT
        As written, this code makes heavy use of UNIX utilities and is
        therefore only supported on UNIX-like environemnts (e.g.
Linux, UNIX, Mac
        OS X).

        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 the configuration file
(cluster.cfg)
        that is generated will have all of the correct parameters. Otherwise,
        you'll need to update the configuration file manually.

        To update the PATH environment variable with the directory
'/usr/local/myapps/bin/',
        update your .bashrc file, thus:

            echo 'export PATH=/usr/local/myapps/bin:$PATH' >> ~/.bashrc.

        Now, every time you open a new terminal window, the PATH environment
        variable will contain '/usr/local/myapps/bin/'. To make your new .bashrc
        file effective immediately (i.e. without having to open a new terminal
        window), use the following command:

            source ~/.bashrc

INSTALLATION
        These installation instructions assume being able to open and use a
        terminal window on Linux.

        (0) Some systems need several dependencies installed ahead of time.

            You may be able to skip this step. However, if subsequent
steps don't
            work, then be sure that some basic libraries are installed, as shown
            below (or ask a system administrator to take care of it). For the
            applicable distribution, open a terminal and then type the
commands as
            indicated:

            For RedHat or CentOS 5.x systems (tested on CentOS 5.5)

                    sudo yum install gcc

            For RedHat or CentOS 6.x systems (tested on "Minimal
Desktop" CentOS 6.0)

                    sudo yum install gcc
                    sudo yum install perl-devel

            For Ubuntu systems (tested on Ubuntu 12-04 LTS)

                    sudo apt-get install curl

            For Debian 5.x systems:

                    sudo apt-get install build-essentials

        (1) Install the non-Perl dependencies:
            (Versions shown are those that we've tested. Please contact us if
            newer versions do not work.)

            Infernal            1.0.2    (http://infernal.janelia.org/)
            MAFFT               6.849b
(http://mafft.cbrc.jp/alignment/software/)
            RNA Vienna package  1.8.4    (http://www.tbi.univie.ac.at/~ivo/RNA/)

            After installing these, make sure all of the foloowing
executables are
            in directories within your PATH:

                cmbuild
                cmcalibrate
                cmsearch
                cmalign
                mafft
                RNAalifold

        (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) Installation method: Use the installer

                  i. Download installer (and name it "installer")

                       curl -o installer -L
http://ircf.rnet.missouri.edu:8000/share.attachment/200


                 ii. Make it executable

                        chmod u+x installer


                iii. Run it.

                        ./installer


            (b) Installation method: Use a CPAN client. Here we demonstrate
                the use of cpanminus to install it to a local Perl module
                directory. These instructions assume absolutely no experience
                with cpanminus.

                  i. Download cpanminus

                        curl -LOk http://xrl.us/cpanm


                 ii. Make it executable

                        chmod u+x cpanm


                iii. Make a local perl5 directory (if it doesn't already exist)

                        mkdir -p ~/perl5


                 iv. Add relevant directories to your PERL5LIB and
PATH environment
                     variables by adding the following text to your ~/.bashrc
                     file:


                        # Set PERL5LIB if it doesn't already exist
                        : ${PERL5LIB:=~/perl5/lib/perl5}

                        # Prepend to PERL5LIB if directory not already
found in PERL5LIB
                        if ! echo $PERL5LIB | egrep -q
"(^|:)~/perl5/lib/perl5($|:)"; then
                            export PERL5LIB=~/perl5/lib/perl5:$PERL5LIB;
                        fi

                        # Prepend to PATH if directory not already found in PATH
                        if ! echo $PATH | egrep -q "(^|:)~/perl5/bin($|:)"; then
                            export PATH=~/perl5/bin:$PATH;
                        fi


                  v. Update environment variables immediately

                        source ~/.bashrc


                 vi. Install Module::Build

                        ./cpanm -l ~/perl5 Module::Build


                vii. Install Bio::App::SELEX::RNAmotifAnalysis

                        ./cpanm -l ~/perl5 Bio::App::SELEX::RNAmotifAnalysis


        Please contact the author if, after consulting this documentation and
        searching Google with error messages, you still encounter difficulties
        during the installation process using one of these two methods.

INCOMPATIBILITIES
        None known

BUGS AND LIMITATIONS
         There are no known bugs in this module.
         Please report problems to molecules <at> cpan <dot> org
         Patches are welcome.

RELATED PUBLICATIONS
        Ditzler et. al. Manuscript currently in review.


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