[med-svn] [Git][med-team/bcbio][master] Updates while appearing on crash space

Steffen Möller gitlab at salsa.debian.org
Fri Aug 2 17:20:14 BST 2019 


Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
e07605b5 by Steffen Möller at 2019-08-02T16:19:28Z
Updates while appearing on crash space

- - - - -


1 changed file:

- debian/TODO


Changes:

=====================================
debian/TODO
=====================================
@@ -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
@@ -211,7 +212,7 @@ package fgbio
   Anyone much into scala?
 
 package manta
-https://github.com/Illumina/manta/
+  https://github.com/Illumina/manta/
   https://salsa.debian.org/med-team/manta
 
 package strelka
@@ -233,5 +234,5 @@ Packages no longer used by bcbio
 --------------------------------
 
 package lumpy
-https://github.com/arq5x/lumpy-sv
+  https://github.com/arq5x/lumpy-sv
 



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/e07605b598378934e116c207dbcf43775177c1db

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/e07605b598378934e116c207dbcf43775177c1db
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