Commit a785f732 authored by Steffen Möller's avatar Steffen Möller
Browse files

Wording, Steffen revisits seqcluster

parent 2e244db1
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+9 −4
Original line number Diff line number Diff line
@@ -2,11 +2,15 @@ TODO for bcbio with Debian
==========================

The following is a list of packages that are used by at least one of the
workflows it aggregates. A complete coverage by Debian of all these tools
workflows bcbio aggregates. A complete coverage by Debian of all these tools
seems increasingly unlikely - their packaging would take longer than the
tools scientific lifespan, i.e. there is a new generation of problem solving
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:

Packages already accepted
------------------------

@@ -64,6 +68,7 @@ package seqcluster
      Some nitty-gritty was going on there wrt Python3 transition
      and an upcoming new release. Needs another review and
      likely some communication with upstream.
         Steffen addresses this.


Packages presumed easy to package
@@ -87,8 +92,8 @@ Package MutliQC - in salsa



Packages of importance for basic NGS workflow well beyond bcbio
---------------------------------------------------------------
Packages of importance for basic NGS workflows with motivation beyond bcbio
---------------------------------------------------------------------------

package mosdepth
  https://salsa.debian.org/med-team/mosdepth