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update paper
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cokelaer committed Aug 6, 2020
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5 changes: 5 additions & 0 deletions doc/joss/paper.bib
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Expand Up @@ -28,6 +28,11 @@ @article{Goodwin2016
year = {2016}
}

@misc{conda,
title = {Conda},
howpublished= {\url{https:/docs.conda.io/en/latest}},
note = "[Online; accessed 4-August-2020]"
}

@article{sequanix:2017,
title = {Sequanix: A Dynamic Graphical Interface for Snakemake Workflows},
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13 changes: 7 additions & 6 deletions doc/joss/paper.md
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Expand Up @@ -25,12 +25,13 @@ bibliography: paper.bib
Next Sequencing Generation (NGS) [@Goodwin2016] implies complex analysis using pipelines that
depends on a plethora of software. A few years ago, setting up a local system to
reproduce an analysis was a challenge even for computer scientists. Indeed, one
needed to be proficient in several languages to compile C/C++ code,
set up the correct JAVA or R environment, etc. Hours were spent in retrieving
the correct source code, days in compilation time, weeks in reproducing analysis. Indeed, one
recurrent issue in research being the ability to reproduce an existing results, which was
difficult with colleagues
working in different environments or different operating system. Nowadays, many solutions are
needed to be proficient in several languages. For instance you would nee to
compile C/C++ code or set up the correct JAVA or R environments just to cite a few examples.
Hours were spent in retrieving the correct source code, days in compilation time, weeks in
reproducing analysis. Reproducing the analysis on another operating system would
have been even more challenging.

Nowadays, many solutions are
available to install reproducible NGS pipelines.
First, the **conda** software manager allows to create environment where compiled version of a
software can be installed. More specifically, the **Bioconda** [Gruning2018] community has
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