Re: PiGx: Pipelines in Genomics

[Steffen Möller <steffen_moeller@gmx.de>]

The dependencies for pigx-rnaseq are now all on salsa, all testing fine.
These are also on med.functional.domains for quick installs. Somewhat
annoying is that the tests of pigx-rnaseq still fail. pigx-rnaseq is on
salsa - please have some fun with it.

My immediate plan is to package more for dependencies for other pigx
workflows and then hope for upstream to investigate failures with me
somewhen later this year. At the moment I am at the single-cell one. The
packaging is easier than for bcbio as the packages drag fewer
dependencies with them.

Best,

Steffen

On 06.08.19 16:18, Steffen Möller wrote:
> 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