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Galaxy wrappers for SARTools (Statistical Analysis of RNA-Seq Tools)

Python 38.76% HTML 15.49% R 45.75%

deseq2 differential-analysis r rna-seq edger reproducible-research galaxy

sartools-galaxy's Introduction

SARTools-Galaxy: a galaxy wrapper for SARTools (Statistical Analysis of RNA-Seq Tools)

Description:

SARTools is a R package dedicated to the differential analysis of RNA-seq data.

SARTools provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis. Note that SARTools does not intend to replace DESeq2 or edgeR: it simply provides an environment to go with them. For more details about the methodology behind DESeq2 or edgeR, the user should read their documentations and papers.

SARTools can be downloaded on github (https://github.com/PF2-pasteur-fr/SARTools). More information about installation can be found at this url.

Requirements using Conda:

Conda is a package manager that among many other things can be used to manage Python packages.

#To install miniconda
#http://conda.pydata.org/miniconda.html
#To install the SARTools R library using conda:
conda install r-sartools
#To set an environment:
conda create -n r-sartools r-sartools`
#To activate the environment:
. activate r-sartools

Test:

planemo test using conda: passed

References:

The SARTools package has been developped at PF2 - Institut Pasteur by M.-A. Dillies and H. Varet ([email protected]).

Thanks to cite H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One, 2016, doi: http://dx.doi.org/10.1371/journal.pone.0157022 when using this tool for any analysis published.

The Galaxy wrapper and scripts have been developped by Loraine Brillet-Guéguen, Institut Français de Bioinformatique

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sartools-galaxy's Issues

pandoc-citeproc not found

After update for Python 3 compatibility, the report.html is no longer generated with following error:

[WARNING] Deprecated: pandoc-citeproc filter. Use --citeproc instead.
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: pandoc document conversion failed with error 83
Execution halted

Can probably be solved with an update of the r-rmarkdown package.

Sartools 1.3.2: problem with a wrong library version of jpeg in conda package R 3.3.1

I open an issue to explain and remember why the git branch version_1_3_2 is not ok yet:

I updated the sartools files for Galaxy to version 1.3.2, with the conda package. But the planemo tests fail when generating the figures with error:

unable to load shared object '/tmp/tmp1qtAns/job_working_directory/000/3/conda-env/lib64/R/modules//R_X11.so':
libjpeg.so.8: cannot open shared object file: No such file or directory

Looking into the job working directory of planemo test in rep conda-env/lib64/, we can find libjpeg.so, libjpeg.so.9, libjpeg.so.9.2.0, but not libjpeg.so.8

This error seems to be due to the R 3.3.1 conda package. See here : ContinuumIO/anaconda-issues#1063

Wrong parsing from RSEM files

Expected error in preSARTools when we have a RSEM file : the parser take the wrong column

Include output tables into the history

Since the tables are only available through a HTML page, it doesn't allow to use those outputs as inputs for some further steps (and within a workflow) like Filter or Graphical tools.
It's a dead-end.

Dataset collection or not Dataset collection? Good question!

Indeed, there are already a bunch of outputs. But I believe that some can be avoid.

table (HTML) : removed because the tables should be included into the history
log (text) : redirected in the stdout because the report is aleady well instructive.
figures : removed because there are already shipped with the report
RData : should be optional?

Galaxy tool sartools_edger fails its tests

The sartools_edger python script executes an R script and then expects two directories to exist: figures and tables. The figures directory exists but the tables directory does not, so the python script fails when trying to copy the contents of tables https://github.com/PF2-pasteur-fr/SARTools-Galaxy/blob/master/sartools/abims_sartools_edger_wrapper.py#L108

The conda environment is active ([email protected], installed 2022-09-22 with conda version 4.12.0) so this could be an issue with the conda environment rather than with this script.