Hello,
bcbio just arrived in the New Queue. Somewhat embarrassingly it does not
install, yet, since python3-seqcluster is still missing who have their
Python3 fixes in their devel branch. I am hoping for an upcoming
official release or will package that branch.
Either way, we are about to have our first workflow package in our
distribution. Now, I would like to test a bunch of research directions
bcbio supports. And tests shall be executed "continuously" (repeatedly)
as we update our packages. We have Debian's CI infrastructure - but
tests run for several hours and our CI infrastructure may not be
perfectly suited for that? Very much so since we are likely to desire
access to the machine to inspect what is going wrong? And not everyone
with a genuine interest is a DD?
Admittedly, what I am more after than "integration testing" is
"knowledge integration". A imagine a site to which Debian Med can log in
and adjust parameters (maybe even in some automated fashion) to have the
same dataset analysed again and again as the reference
databases/software underneath matures/develops, preferably with some
gold standard as a reference or some easy access to the same material
for labs around the world to prove stuff - this may turn out to be
interesting. And when there alternative workflows arriving in our
distro, like with GATK, this may become even more interesting. Setup and
maintenance would need to be completely automated - we just don't have
time for anything else.
I was offered a 2x6-core 64GB (I know) server with rack space. It has a
2TB drive and slots to add more. That we could play with.
Comments?
Best,
Steffen
-------- Forwarded Message --------
Subject: bcbio_1.1.2-2_amd64.changes is NEW
Date: Mon, 21 Jan 2019 23:19:26 +0000
From: Debian FTP Masters <ftpmas...@ftp-master.debian.org>
To: Steffen Moeller <moel...@debian.org>, Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
binary:bcbio is NEW.
binary:python3-bcbio is NEW.
binary:bcbio is NEW.
binary:python3-bcbio is NEW.
source:bcbio is NEW.
bcbio_1.1.2.orig.tar.gz is only available in NEW.
bcbio_1.1.2.orig.tar.gz is only available in NEW.
Your package has been put into the NEW queue, which requires manual action
from the ftpteam to process. The upload was otherwise valid (it had a good
OpenPGP signature and file hashes are valid), so please be patient.
Packages are routinely processed through to the archive, and do feel
free to browse the NEW queue[1].
If there is an issue with the upload, you will receive an email from a
member of the ftpteam.
If you have any questions, you may reply to this email.
[1]: https://ftp-master.debian.org/new.html
or https://ftp-master.debian.org/backports-new.html for *-backports
