[med-svn] [Git][med-team/bcbio][master] Update, mention crash space

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
7cee64ad by Steffen Möller at 2019-08-03T14:34:01Z
Update, mention crash space

- - - - -


1 changed file:

- debian/TODO


Changes:

=====================================
debian/TODO
=====================================
@@ -7,9 +7,18 @@ seems increasingly unlikely - their packaging would take longer than the
 tools' scientific lifespan, i.e. there is a new generation of problem solving
 emerging and/or the workflow as a whole will have mutated in the meantime.
 
-We yet have to find an answer to this challenge. For quite some this is to
-just go and use Conda. We should also consider mixing Conda with Debian,
-though. But let us first see where we are with bcbio:
+We yet have to find an answer to this challenge.  A series of repositories
+of packages that are still waiting in the new queue for their acceptance
+in the distribution is available as
+
+ deb http://med.functional.domains/r unstable main contrib non-free
+ deb http://med.functional.domains/med unstable main contrib non-free
+ deb http://med.functional.domains/python unstable main contrib non-free
+ deb http://med.functional.domains/science unstable main contrib non-free
+
+Anyway, for quite some this is to just go and use Conda.  We should also
+consider mixing Conda with Debian, though. But let us first see where
+we are with bcbio:
 
 Packages already accepted
 ------------------------
@@ -98,6 +107,10 @@ package python-seqcluster (in crash space)
        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
 
+python3-dateutils (in new queue) (in crash space)
+  https://salsa.debian.org/python-team/modules/python-dateutils
+    Needed by python-seqcluster - actually I am not 100% sure about where in the latest version of seqcluster that is
+
 package viennarna (in crash space)
     https://github.com/ViennaRNA/ViennaRNA
     https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog
@@ -110,7 +123,7 @@ package viennarna (in crash space)
     Python and Perl packages are not functional, yet, not needed for seqcluster
     Waiting for acceptance of cthreadpool.
 
-Package MutliQC - (in crash space)
+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
@@ -155,15 +168,18 @@ package mosdepth
   of which the first already is in the new queue
 
 package oncofuse
-   https://salsa.debian.org/med-team/oncofuse
+  https://salsa.debian.org/med-team/oncofuse
+    Stuck over typical Java issue
 
 package optitype
   https://salsa.debian.org/med-team/optitype (rudimentary)
+    Stuck over too many dependencies
 
 package vcfanno
   https://salsa.debian.org/med-team/vcfanno
   Not fun because of many GO packages that are still missing,
   "biogo" being one of them.
+    Stuck over too many dependencies
 
 
 



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/7cee64ad75f23d4a1bd6c680098791c6708ea262

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/7cee64ad75f23d4a1bd6c680098791c6708ea262
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