Re: PiGx: Pipelines in Genomics

[Steffen Möller <steffen_moeller@gmx.de>]

Hello again,

I packaged everything that was missing for pigx-rnaseq and put it into
salsa.

Some bcbio/debian/TODO analogon of where we are I put in
https://salsa.debian.org/med-team/pigx-rnaseq/blob/master/debian/TODO
Most bits are already uploaded, except for tximport and pigx-rnaseq itself.

The developer's version of tximport does not have that jquery problem
what I see, but no release tags. So I have asked for these and see how
things go. Over the next days I think I will rebuild that all on the
med.functional.domains and, should the tests work out fine, then likely
address the single-cell variant of it.

Best,

Steffen

On 05.08.19 21:04, Steffen Möller wrote:
> Hello,
>
> I was just pointed to PIGx (https://bioinformatics.mdc-berlin.de/pigx/ ,
> https://doi.org/10.1093/gigascience/giy123 ) that offers several
> pipelines for "next generation" sequencing:
>
>   *
>
>     PiGx BSseq <https://github.com/BIMSBbioinfo/pigx_bsseq> for raw
>     fastq read data of bisulfite experiments
>
>   *
>
>     PiGx RNAseq <https://github.com/BIMSBbioinfo/pigx_rnaseq> for RNAseq
>     samples
>
>   *
>
>     PiGx scRNAseq <https://github.com/BIMSBbioinfo/pigx_scrnaseq> for
>     single cell dropseq analysis
>
>   *
>
>     PiGx ChIPseq <https://github.com/BIMSBbioinfo/pigx_chipseq> for
>     reads from ChIPseq experiments
>
>   *
>
>     PiGx CRISPR <https://github.com/BIMSBbioinfo/pigx_crispr> /(work in
>     progress)/ for the analysis of sequence mutations in CRISPR-CAS9
>     targeted amplicon sequencing data
>
> It ships with test scripts and data. Their package management is with
> GUIX. Anyway, this could be something for us to get some "we can
> workflow"-stamp before we have bcbio done. I looked at
> https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/master/requirements.txt and
> https://github.com/BIMSBbioinfo/pigx_scrnaseq/blob/master/requirements.txt
> which does not look too bad. I have just packaged a few dependencies for
> it that we did not have with us, yet (trim_galore, the CRAN packages
> corrplot (very nice, did not know about that one) and gProfiler (long
> overdue)), and now I am a bit stuck on the BioConductor package
> tximport, see separate email. But it very much seems like we are getting
> there very quickly.
>
> Best,
>
> Steffen
>