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 >
