[Debian-med-packaging] Bug#903911: ITP: pilon-non-free -- automated genome assembly improvement and variant detection tool

[Andreas Tille]

Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille at debian.org>

* Package name    : pilon-non-free
  Version         : 1.22
  Upstream Author : Copyright: Copyright 2012-2017 Broad Institute, Inc.
* URL             : https://github.com/broadinstitute/pilon/wiki
* License         : GPL-2
  Programming Lang: Java
  Description     : automated genome assembly improvement and variant detection tool
 Pilon is a software tool which can be used to:
  * Automatically improve draft assemblies
  * Find variation among strains, including large event detection
 Pilon requires as input a FASTA file of the genome along with one or more
 BAM files of reads aligned to the input FASTA file. Pilon uses read
 alignment analysis to identify inconsistencies between the input genome and
 the evidence in the reads. It then attempts to make improvements to the
 input genome, including:
  * Single base differences
  * Small indels
  * Larger indel or block substitution events
  * Gap filling
  * Identification of local misassemblies, including optional opening
    of new gaps
 .
 The code of pilon is actually free but currently there is no method
 to build the JAR from the scala source in Debian.  This package is
 supposed to be replaced by a pilon package once it can be build from
 source (see bug #873341).

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/pilon-non-free
It is planed to replace this package pilon-non-free by a pilon
package once sbt will be usable again (see #873341).  Unfortunately
it is expected that this will take way longer than expected
(see the discussion on debian-java list).