debian/TODO

@@ -13,15 +13,16 @@ 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/nim 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:
+Anyway, for quite some of our users 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
-------------------------
+-------------------------
 
 Are no longer shown in this list but are added to the dependencies of
 bcbio.
@@ -36,10 +37,6 @@ package pizzly (in new queue) (in crash space)
 package r-wasabi (in new queue) (in crash space)
    https://salsa.debian.org/r-pkg-team/r-other-wasabi
 
-package tophat-recondition (in new queue) (in crash space)
-  https://github.com/cbrueffer/tophat-recondition
-  https://salsa.debian.org/med-team/tophat-recondition
-
 package libjs-scribl (in new queue) (in crash space)
   https://salsa.debian.org/med-team/libjs-scribl
   http://chmille4.github.io/Scribl/
@@ -60,11 +57,10 @@ package pyomo (in crash space)
     needed by optitype
     Status: Builds if errors in build time tests will be ignored
 
-package pyutilib (in crash space)
+package pyutilib (in new queue) (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 python-seqcluster (in crash space)
    https://github.com/lpantano/seqcluster/
@@ -82,7 +78,6 @@ package python-seqcluster (in crash space)
 
 
      Additional requirements:
-      python3-dateutils (in new queue)
       python3-pytz ----> packaged but under the name python3-tz
 
      And there are R packages that should be recommended at least (from https://github.com/lpantano/seqcluster/blob/master/scripts/install_libraries.R)
@@ -96,10 +91,6 @@ 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

debian/control

@@ -46,6 +46,7 @@ Build-Depends: debhelper (>= 10),
                seqtk,
                tabix,
                tophat,
+               tophat-recondition,
                wham-align,
                xonsh,
 # documentation
@@ -119,7 +120,9 @@ Suggests: toil,
 # for cancer heterogeneity analysis with BubbleTree
           libglu1-mesa,
 # for low mem instead of rna-star
-          tophat2
+          tophat2,
+# found in source code but not exactly sure about its importance
+          tophat-recondition
 Description: toolkit for analysing high-throughput sequencing data
  This package installs the command line tools of the bcbio-nextgen
  toolkit implementing best-practice pipelines for fully automated high