Commit ce7a2658 authored by Steffen Möller's avatar Steffen Möller
Browse files

seqcluster keeps making trouble

parent b6021c6d

debian/TODO

+38 −1
Original line number Diff line number Diff line
@@ -75,13 +75,36 @@ package seqcluster 
       ./.travis.yml:- conda install --yes -c conda-forge -c bioconda memory_profiler openjdk pysam pybedtools pandas numpy biopython progressbar2 pyyaml bedtools samtools mirtop viennarna -q

      so, for some successful testing it seems like we need viennarna, still. That is not yet in the distribution. If truly dependending on it then bcbio ends up in contrib.



     seqcluster redistributes a "Free as in beer" graph library in its source tree at ./misc/js/amcharts.js that upstream accepts to be substituted with references to the online location in a CDN.  Steffen will address that. Downside of it all: seqcluster needs to go to contrib.



     Additional requirements:

      python3-dateutils (not yet packaged)

      python3-pytz (not yet packaged)



     And there are R packages that should be recommended at least (from https://github.com/lpantano/seqcluster/blob/master/scripts/install_libraries.R)

       # We cover all CRAN packages

       # Most BioC packages are missing - even edgeR ? :

       r-bioc-edgeR - missing

       r-bioc-HTSFilter - missing

       r-bioc-DEGreport - missing

       # novel packages

       install.github("hbc/CHBUtils") - missing

       install.github("lpantano/isomiRs", "master") - missing

       install_github('rstudio/rmarkdown')  -- this may be the same we have from CRAN - not checked



package viennarna

    https://github.com/ViennaRNA/ViennaRNA

    https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog

       No idea about where exactly we stand with this.

       The package now has a custom license file - redistributable but non-free.

    Needed for testing seqcluster.

	Steffen revisits ViennaRNA

	Steffen revisits ViennaRNA, will update to new upstream version this weekend

           Does not compile - source tree seems incomplete (RNAfold_cmdl.c missing)

           External dependencies json (in Debian, I think, can otherwise be deconfigured) and cthreadpool (not yet in Debian) need to be addressed



package cthreadpool

   https://github.com/Pithikos/C-Thread-Pool/blob/master/thpool.h

      Needed by ViennaRNA



Packages presumed easy to package

---------------------------------
@@ -107,6 +130,20 @@ Package MutliQC - in salsa 
   https://salsa.debian.org/med-team/multiqc

    Steffen will address this one



r-bioc-edgeR

   https://tracker.debian.org/pkg/r-bioc-edger

	This was removed from buster in February - a bit of a bummer, I tend to think

   https://salsa.debian.org/r-pkg-team/r-bioc-edger

   https://bioconductor.org/packages/release/bioc/html/edgeR.html

     Needed by seqcluster



r-bioc-HTSFilter

   https://bioconductor.org/packages/release/bioc/html/HTSFilter.html

     Needed by seqcluster



r-bioc-DEGreport

   https://bioconductor.org/packages/release/bioc/html/DEGreport.html

     Needed by seqcluster





Packages of importance for basic NGS workflows with motivation beyond bcbio