Commit e07605b5 authored by Steffen Möller's avatar Steffen Möller
Browse files

Updates while appearing on crash space

parent ccf71830

debian/TODO

+50 −49
Original line number Diff line number Diff line
@@ -20,47 +20,60 @@ bcbio. 
Packages already in the New Queue

---------------------------------



package atropos

  https://salsa.debian.org/med-team/atropos (in new queue)

package atropos (in new queue) (in crash space)

  https://salsa.debian.org/med-team/atropos



package bamtofastq from biobambam2

  https://salsa.debian.org/med-team/biobambam2 (in new queue)

package bamtofastq from biobambam2 (in new queue) (in crash space)

  https://salsa.debian.org/med-team/biobambam2



package kallisto (in new queue)

package kallisto (in new queue) (in crash space)



package pizzly

   https://github.com/pmelsted/pizzly (in new queue)

package pizzly (in new queue) (in crash space)

   https://github.com/pmelsted/pizzly

   https://salsa.debian.org/med-team/pizzly



package r-wasabi

   https://salsa.debian.org/r-pkg-team/r-other-wasabi (in new queue)

package r-wasabi (in new queue) (in crash space)

   https://salsa.debian.org/r-pkg-team/r-other-wasabi



package tophat-recondition

  https://github.com/cbrueffer/tophat-recondition (in new queue)

package tophat-recondition (in new queue) (in crash space)

  https://github.com/cbrueffer/tophat-recondition

  https://salsa.debian.org/med-team/tophat-recondition



package gffread

  https://salsa.debian.org/med-team/gffread (in new queue)

package gffread (in new queue but FTBFS)

  https://salsa.debian.org/med-team/gffread



package libjs-scribl (in new queue) (in crash space)

  https://salsa.debian.org/med-team/libjs-scribl

  http://chmille4.github.io/Scribl/

    A surprisingly neat JavaScript library to show genomic features

       Needed for DFSG-compliance of seqcluster



package cthreadpool (in new queue) (in crash space)

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

      Needed by ViennaRNA



Packages just waiting for someone addressing the last mile for the upload

-------------------------------------------------------------------------



package pyomo

package pyomo (in crash space)

  https://github.com/Pyomo/pyomo

  https://salsa.debian.org/science-team/pyomo

    build-deps on pyutilib

    needed by optitype

    Status: Builds if errors in build time tests will be ignored



package pyutilib

package pyutilib (in crash space)

  https://github.com/PyUtilib/pyutilib

  https://salsa.debian.org/python-team/modules/pyutilib

    needed by pyomo for testing

    Status: Builds if errors in build time tests will be ignored



package seqcluster

   https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz

package python-seqcluster (in crash space)

   https://github.com/lpantano/seqcluster/

   https://salsa.debian.org/med-team/python-seqcluster

      The Python3 transition seems fine now. Weird, though,

      the test takes too long / something hangs.

      The Python3 transition seems fine now.

      The package needs RNAfold fof the ViennaRNA package for testing. Otherwise it stalls without an error message.

      Dependencies are incomplete / an update wrecked the one immaculate testing.

      When grepping for "conda install":

       ./doc/source/installation.rst:    ~/install/seqcluster/anaconda/conda install seqcluster seqbuster bedtools samtools pip nose numpy scipy pandas pyvcf -c bioconda

       ./Dockerfile:     conda install --yes -c conda-forge -c bioconda scipy seqcluster bedtools samtools pip nose setuptools -q && \
@@ -69,7 +82,6 @@ package seqcluster 


     seqcluster accepted a patch to eliminate a "Free as in beer" graph library from its source tree at ./misc/js/amcharts.js. These are now references to the online location in a CDN.



     The package builds with testing if RNAfold of the ViennaRNA package is present. Otherwise it stalls without an error message.



     Additional requirements:

      python3-dateutils (in new queue)
@@ -78,41 +90,34 @@ package seqcluster 
     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 - Depends DESeq and edgeR which both in turn depend locfit which makes all non-free

       r-bioc-DEGreport - all pre-depends except edgeR are in new

       apparently optional for bcbio: r-bioc-edgeR - missing

       apparently optional for bcbio: r-bioc-HTSFilter - Depends DESeq and edgeR which both in turn depend locfit which makes all non-free

       apparently optional for bcbio: r-bioc-DEGreport - all pre-depends except edgeR are in new

       # novel packages

       install.github("hbc/CHBUtils") - Uploaded to new as r-other-chbutils_0.1+git20171026.a226cee-1

       r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new

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

       apparently optional for bcbio: install.github("hbc/CHBUtils") - Uploaded to new as r-other-chbutils_0.1+git20171026.a226cee-1

       apparently optional for bcbio: r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new

       apparently optional for bcbio: install_github('rstudio/rmarkdown')  -- this may be the same we have from CRAN - not checked



package viennarna

package viennarna (in crash space)

    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, will update to new upstream version this weekend

           Does not compile

           External dependencies

              json (in Debian, I think, can otherwise be deconfigured)

              cthreadpool (uploaded)

           It now mostly compiles.

           Better use current master than release because of erroneous commits of autogenerated files in 2.4.13 release source tree.



package cthreadpool (in new queue)

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

      Needed by ViennaRNA

           Using current master not release because of erroneous commits of autogenerated files in 2.4.13 release source tree.

           Manual removal of folders along instructions in d/copyright

    Python and Perl packages are not functional, yet, not needed for seqcluster

    Waiting for acceptance of cthreadpool.



Package MutliQC - (in crash space)

   https://salsa.debian.org/med-team/multiqc

   Not redistributable until we have removed the highcharts library from that source tree

     https://github.com/ewels/MultiQC/issues/800



Packages presumed easy to package

---------------------------------



package Scribl

  http://chmille4.github.io/Scribl/

    A surprisingly neat JavaScript library to show genomic features

       Needed for seqcluster

   In new queue as libjs-scribl



package gjh_asl_json

  https://github.com/ghackebeil/gjh_asl_json

    needed by pyomo for testing
@@ -125,10 +130,6 @@ package "asl solver" 
  http://www.ampl.com/netlib/ampl/solvers.tgz

    needed by gjh_asl_json



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