[med-svn] [Git][med-team/bcbio][master] seqcluster keeps making trouble

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
ce7a2658 by Steffen Möller at 2019-06-24T14:58:16Z
seqcluster keeps making trouble

- - - - -


1 changed file:

- debian/TODO


Changes:

=====================================
debian/TODO
=====================================
@@ -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



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/ce7a2658d980cc9af0179214c46870202294c69b

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/ce7a2658d980cc9af0179214c46870202294c69b
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