Tiger Team Projects

The following enumeration provides an overview of collaborations between members of the bwHPC-S5 team and scientists, i.e. tiger teams. To apply for support by a tiger team, click

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Tiger Team: tt-shortran

Deployment of Shortran Pipeline on BinAC using Singularity

Shortran [1] is a pipeline for plant or animal small RNA-seq data analysis. Shortran works well for the lotus species. The pipeline has many dependencies (Python, Perl, blast, MySQL, some additional tools) and is rather old (2012). Partly, the pipeline requires old versions of the dependencies, therefore it is not possible to install it directly on the HPC-cluster. The Tiger-Team's goal was the creation of an executable and well documented Singularity container [2], which contains all dependencies and the pipeline. We deployed the pipeline together with all dependencies as a Singularity container. The pipeline wrote to folders that are not writable in the container, so we had to change some input and output paths of the pipeline. In the end pipeline was tested successfully by the user.

[1] Gupta, V., Markmann, K., Pedersen, C. N. S., Stougaard, J., & Andersen, S. U. (2012). Shortran: A pipeline for small RNA-seq data analysis. Bioinformatics, 28(20), 2698–2700. https://doi.org/10.1093/bioinformatics/bts496 [2] Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PLOS ONE, 12(5), 1–20. https://doi.org/10.1371/journal.pone.0177459

Members of the Tiger-Team: ZMBP, Universität Tübingen; HPC-Kompentenzzentrum BinA

Status: finished.