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Galaxy wrappers for SARTools (Statistical Analysis of RNA-Seq Tools)
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.
The Preprocess tool should for me just generate the target file and let SARTools deal with the tables.
Furthermore, Preprocess can be interesting for some other tools which need a target file (I'm thinking about a tool in the W4M workflow)
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.
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
Travis tests are broken. See https://travis-ci.org/PF2-pasteur-fr/SARTools-Galaxy/builds/232387997
When merged (15th May), the tests where fine. It was with R 3.3.1. Now they are broken with R 3.3.2.
I am investigating.
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.
Expected error in preSARTools when we have a RSEM file : the parser take the wrong column
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