Bug#958172: ITP: virusseeker-virome -- Mine sequence data to identify sequences of microbial origin
Package: wnpp
Severity: wishlist
Owner: Debian Med Team <debian-med@lists.debian.org>
* Package name : virusseeker-virome
Version : 0.063
Upstream Author : Guoyan Zhao, Washington University, St. Louis, MO.
* URL : https://wupathlabs.wustl.edu/virusseeker/
* License : GPL-3+
Programming Lang: Perl
Description : Mine sequence data to identify sequences of microbial origin
VirusSeeker is a set of fully automated and modular software package designed
for mining sequence data to identify sequences of microbial origin. The
pipeline was optimized for analysis of data generated by the Illumina next
generation sequencing platform but can be applied to data generated by other
platforms as well.
.
VirusSeeker first identifies candidate viral sequences by comparing with
virus-only databases and then identify true viral sequences by comparing the
candiate viral sequences to NCBI NT and NR databases. Microbial sequences are
identified on the basis of BLAST alignments and the taxonomic classification
of the reference sequence(s) to which a read is aligned. Viruses are the
focal point of VirusSeeker as released.
________________________________________________________________
Greetings,
I intend to give a hand to the Debian Med Team with the
packaging of the software VirusSeeker-Virome, which is part of
the VirusSeeker suite, itself beeing part of the Covid-19 list
of packages needing work established by the Med team:
https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work
A repository for working on the packaging has been opened on
Salsa at the following location, and contains a stub of Debian
source code packaging:
https://salsa.debian.org/med-team/virusseeker-virome
It is worth noting that the upstream author has apparently
opened a public Git repository for VirusSeeker-Virome:
https://github.com/guoyanzhao/VirusSeeker-Virome
Contrary to the package provided on wupathlabs.wustl.edu, this
repository is dfsg compliant, which is good news (the current
release ships with a bunch of old scripts licensed under OSL-2.1
apparently not compatible with the GPL-3+). However, it seems
still work in progress for the moment, as there are no releases
or tags to hang on yet.
Kind Regards,
--
Étienne Mollier.
Reply to: