pervouchine / ipsa-full

Integrative Pipeline for Splicing Analyses (IPSA)

Copyright 2014 Dmitri Pervouchine ([email protected]), Lab Roderic Guigo Bioinformatics and Genomics Group @ Centre for Genomic Regulation Parc de Recerca Biomedica: Dr. Aiguader, 88, 08003 Barcelona

This file is a part of the 'ipsa-full' package. 'ipsa-full' package is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

'ipsa-full' package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with 'ipsa-full' package. If not, see http://www.gnu.org/licenses/.

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Integrative Pipeline for Splicing Analyses (IPSA)

** This is a full version. A short version is available here https://github.com/pervouchine/ipsa**

• DISCLAIMER

  Software and documentation in this release are very preliminary. Currently the pipeline is configured to download a few BAM files and run all computations for them, as an example.

• SYNOPSIS

The integrative pipeline for splicing analyses does:

• Quantification of splice junctions and splice boundaries

• Calculation of splicing indices, exon- and intron-centric

• Analysis of micro-exons and local splice-graph structure

• DEPENDENCIES

• maptools (automatic from https://github.com/pervouchine/maptools)

• sjcount (automatic from https://github.com/pervouchine/sjcount)

• samtools (needed by sjcount, automatic from http://sourceforge.net/projects/samtools/files/samtools/0.1.18/)

• R-statistics (http://www.r-project.org/)

• ggplot2 (http://ggplot2.org/)

• Perl standard modules (http://www.perl.org/)

• INSTALLATION

To install, do

git clone https://github.com/pervouchine/ipsa-full
cd ipsa-full
make all

• EXAMPLES

An example of a pipeline buildout is available by running

make -f example.mk all

• DOCUMENTATION

The documentation on the pipeline components is available in latex/ subdirectory The documentation on the sjcount utility is available in sjcount/latex/ subdirectory

ipsa-full's Issues

Problem installing under Ubuntu

I tried to install the program in Ubuntu and Mac OS X. It has no problems installing in Mac OS X but under Ubuntu the installation stops with the following error:

make[1]: Entering directory `/genedata/Resources/Software/ipsa-full/sjcount-full-3.1'
g++ -I samtools-0.1.18/ j_count.c progressbar.o samtools-0.1.18/libbam.a -lz -o j_count
j_count.c: In function ‘int main(int, char**)’:
j_count.c:255:80: error: conditional expression between distinct pointer types ‘gzFile’ and ‘FILE* {aka _IO_FILE*}’ lacks a cast
         ssj_file = zipped ? gzopen(ssj_file_name,"w") : fopen(ssj_file_name,"w");
                                                                                ^
make[1]: *** [j_count] Error 1
make[1]: Leaving directory `/genedata/Resources/Software/ipsa-full/sjcount-full-3.1'
make: *** [sjcount-full-3.1/sjcount] Error 2

Installation issue: Can't locate Perl/utils.pm in @INC

Hello, I'm trying to install the package. Here is what I did: http://nbviewer.ipython.org/gist/olgabot/1f48a7e73966394464c7

I ran into an error with Perl, and I'm a Perl newbie so this error is hard for me to interpret.

perl Perl/make.pl -repository example/input/ -dir example/output/ -group idrGroup -param '-read1 0' -annot example/hg19v18.gff -genome example/hg19 -merge pooled < example.dat > example.mk
Can't locate Perl/utils.pm in @INC (@INC contains: /opt/biotools/miRDeep2/share/perl5 /opt/biotools/ViennaRNA/lib64/perl5 /projects/ps-yeolab/software/ActivePerl-5.16/site/lib /projects/ps-yeolab/software/ActivePerl-5.16/lib .) at Perl/make.pl line 2.
BEGIN failed--compilation aborted at Perl/make.pl line 2.
make: *** [example.mk] Error 2

After searching around, it seems like the utils.pm file should have come with this module, but Perl can't find it.

Can you help me out? I'm excited to try out this package!
Thanks!
Olga

PS: It would be helpful to have example output figures in the github repo README itself, so someone can see the possibilities of your package without having to install it first.