Re: Shared cluster storage for bioinformatics

[Tony Travis]

On 24/07/2024 12:13, Urmas Rist wrote:

I followed this up and took a look at the "SaunaFS" GitHub" repo:



https://github.com/aNeutrino/open-saunafs


Quick correction: The official repository is here:


https://github.com/leil-io/saunafs


Hi, Urmas.

Sorry - Thanks for correcting my mistake,

  Tony.

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Shared cluster storage for bioinformatics

[Tony Travis]

Hi, Andreas.

As you might remember, I've been using and advocating the "LizardFS" SDS 
(Software Defined Storage) filesystem as shared cluster storage for my 
bioinformatics work for a long time. I used it for many years on the HPC 
cluster I built at the Mario Negri Institute in Milan and on my servers 
in Italy. I'm currently using "LizardFS" at AAU (Assam Agricultural 
University) in India and also on my own 'Garage' cluster in Scotland.


However, I've become increasingly worried about the abrupt removal of 
"LizardFS" from Debian/Ubuntu repositories because of FTCFS errors and, 
in particular, long-term support for the research group I work for at 
AAU. So, I've been looking for an alternative SDS cluster filesystem.


I've looked at several SDS alternatives but, recently, I found out about 
"SaunaFS" in a comment on the "LizardFS" repo:



https://github.com/lizardfs/lizardfs/issues/805#issuecomment-2238866486


I followed this up and took a look at the "SaunaFS" GitHub" repo:


https://github.com/aNeutrino/open-saunafs


This looks promising as a replacement for "LizardFS" and, today, I had a 
meeting online with Aleksandr Ragel and the "SaunaFS" team at "leil 
Storage":



https://leil.io/


This company sells storage hardware and, when "LizardFS" ceased trading, 
they hired some of the former "LizardFS" developers to work for them on 
"SaunaFS":



https://saunafs.com/


This is NOT a version of "LizardFS", but "SaunaFS" does use some of the 
code from "LizardFS" and is being developed as a completely open-source 
filesystem that underpins their commercial storage products and paid for 
commercial support.


During our conversation, I asked Aleksandr if they plan to issue an RFP 
(Request for Packaging) for Debian/Ubuntu. I've already compiled my own 
'unofficial' deb's from their GitHub sources under Ubuntu 22.04 LTS. 
However, at present, the official "SaunaFS" deb's are only available on 
request from their company's private repo.


Whilst I realise that this is not quite within your remit as the leader 
of the "Debian-Med" project I believe that people who use your packages 
might be interested in "SaunaFS" as shared storage for bioinformatics.


If Aleksandr or one of the "SaunaFS" team post an RFP to:


https://wiki.debian.org/WNPP


Would you, as a Debian Developer, be willing to take an interest, or ask 
another developer who might be interested?


Thanks,

  Tony.

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Re: Any input for some talk about usage of Debian in HPC

[Tony Travis]

On 20/05/2024 21:00, Steven Robbins wrote:

Hello,

On Sunday, May 19, 2024 9:31:02 A.M. CDT Tony Travis wrote:


You can't ignore the host OS when you talk about HPC applications and
the HEP (High Energy Physics) community put a lot of effort into
developing good node provisioning systems and job-scheduling for HPC.
Consequently, there was a significant bias towards support for HEP
applications running under CentOS and less support for bioinformatics.


I've been out of academia for decades, but HEP was my first love and
neuroimaging my second, so this paragraph really piqued my interest.  Can you
briefly say what are the different needs of HEP and bioinformatics and how they
are in conflict?


Hi, Steve.

Many HEP applications involve a lot of floating-point arithmetic and are 
computationally intensive. By contrast most bioinformatics applications 
do not require floating point arithmetic: They are dominated by speed of 
memory access and memory size. Optimisations used in HEP calculations to 
keep everything in the high-speed CPU cache don't help with this access.


One area of bioinformatics in particular that has this sort of memory 
requirement is sequence alignment and sequence assembly. Some efforts 
have been made to speed this up using GPGPU and SIMD CPU instructions, 
but I've found it all very complicated and disappointing to be honest.


A recent success for GPGPU applications in bioinformatics is, however, 
base-calling of 'long' DNA sequencing reads and TensorFlow ML (Machine 
Learning) methods for error-correcting DNA/RNA sequence reads and e.g. 
predicting Transcription Factor Binding Sites etc.


None of this requires the use of floating point calculations in the 
frequency/Fourier domain that many HEP applications do. I must admit 
that my views are largely based on experience of helping my friend do 
DFT (Density Field Theory) simulations of protein 'docking' domains on a 
Beowulf cluster that we built for chemical modelling and bioinformatics!


I also worked for several years doing image analysis with Physicists :-)

Bye,

  Tony.

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Re: Any input for some talk about usage of Debian in HPC

[Tony Travis]

On 19/05/2024 12:12, Andreas Tille wrote:

Hi,

I have an invitation to have some talk with the title

Debian GNU/Linux for Scientific Research

Abstract:

Over the past decade, Enterprise Linux has dominated large-scale
research computing infrastructure. However, recent developments have
sparked increased interest in community-led alternatives. Debian
GNU/Linux, a long-standing choice among researchers for supporting
scientific work, is experiencing a renewed interest for High-Throughput
Computing (HTC) and High-Performance Computing (HPC) applications.  This
presentation will provide an overview of how Debian is being utilized to
support scientific research and will include a case study showcasing the
migration of HTC operations from Enterprise Linux 7 (EL7) to Debian.

While I could talk about Debian Science and Debian Med in general it
would be cool to reference to some real life examples where Debian is
used in Science and what might be the reason to use Debian.


Hi, Andreas.

The Sanger Centre in the UK use Ubuntu + OpenStack + Ceph:

https://www.sanger.ac.uk/group/core-software-services/

I realise that it's not Debian, but it is based on Debian. I went there 
many years ago when they were running Debian on DEC Alpha AXP's, but 
they moved to CentOS because many other Academic HPC centres were using 
it, including ours when I worked at the University of Aberdeen.


This was not a good experience, and they decided to change to Ubuntu 
mainly because of the support provided by Canonical for OpenStack and 
Ceph. However, in my opinion, CentOS/RHEL is not a good platform for 
bioinformatics because the 'Enterprise' approach stifles innovation.


You can't ignore the host OS when you talk about HPC applications and 
the HEP (High Energy Physics) community put a lot of effort into 
developing good node provisioning systems and job-scheduling for HPC. 
Consequently, there was a significant bias towards support for HEP 
applications running under CentOS and less support for bioinformatics.


This was partly the motivation underlying our development of Bio-Linux 
in order to provide biologists with an alternative platform running on 
their own hardware instead of struggling to get the IT department to 
port the software they wanted to use to CentOS. In that respect the 
Debian-Med project was fundamentally important in helping biologists do 
their work outside of the centrally managed 'Enterprise' oriented IT 
policy imposed on us by Universities and Research Institutes.


The Sanger Centre provide a centrally managed HPC that is 
'biologist-friendly' and, I think, is an excellent model of how it 
should be done. However, it does not support the view that Debian should 
be the HPC OS because the main reason they chose Ubuntu was the 
commercial support for OpenStack and Ceph provided by Canonical.



I personally would like to stress the "we package what we use" aspect
and the "we mentor upstream to merge competence of the program with
packaging skills" idea.  Any input would be welcome to cover more ideas.


As you might remember, I built and I advocate the use of 'departmental' 
or 'research-group' clusters. These are much more powerful than an 
individual biologists personal laptop, but are under the administrative 
control of the department or research group that funded their purchase.


In the past, I've used various HPC node-provisioning, cluster filesystem 
and job submission systems running under one version of another of 
Bio-Linux, now using your "med-bio" meta-package to provide 
bioinformatics software instead of the discontinued Bio-Linux packages.


However, I've recently set up a 3-node 'Proxmox-VE' cluster:


https://www.proxmox.com/en/proxmox-virtual-environment/overview


[Proxmox is a GPL server management system based on Debian]

I'm using the Proxmox cluster for a bioinformatics in schools project 
with the University of Edinburgh:



https://4273pi.org/


I'm also planning to use it for a new project with the IAEA in Vienna.

I think that giving biologists the choice of running the software they 
want under the OS they choose is very important when innovation is the 
priority of an organisation rather than centralisation of IT systems to 
reduce cost. You can, of course use Proxmox-VE as the node-provisioning 
and shared filesystem of an HPC cluster. Or, simply provide biologists 
with VMs running their OS of choice, administered by themselves e.g. a 
Bio-Linux VM or vanilla Debian etc. etc.


Finally, don't forget about Amdahl's Law:


https://en.wikipedia.org/wiki/Amdahl%27s_law


There is really no such thing as an HPC or HTP 'application', because 
it's the underlying resource management system of an HPC cluster that 
provides the 'HP'. In my experience, most bioinformatics applications 
are 'embarrassingly' parallel and in this case processes do not 
communicate with each other. The 'HP' is achieved by managing the 
workflow efficiently 

Re: User input needed: Stop supporting 32 bit architectures with emboss (Was: emboss-lib: identified for time_t transition but no ABI in shlibs)

[Tony Travis]

On 31/01/2024 10:08, Andreas Tille wrote:

[...]
running 32bit systems?  Can you forward this question to them?  Or more
generally:  Wouldn't it make sense if people doing Debian based
bioinformatics would subscribe this list and speak here?


Hi, Andreas.

Yes, you're right, and I've forwarded your email...

Thanks,

  Tony.

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Re: User input needed: Stop supporting 32 bit architectures with emboss (Was: emboss-lib: identified for time_t transition but no ABI in shlibs)

[Tony Travis]

On 31/01/2024 06:53, Andreas Tille wrote:

Hi again,

besides my suggested solution to split up emboss-lib again (and when
doing so make the package emboss-lib a metapackage depending from single
packages to match all its rdepends) I wonder whether we should provide
EMBOSS for 64 bit architectures only.  While we probably need to file a
lot of removal requests to 32 bit packages of its rdepends it somehow
fits the reality that these days nobody seriously runs emboss on 32bit
architectures.  As explained in the according wiki page[1] other binary
distros are dropping 32-bit at all and Debian rather cares for
automotive, IOT, TVs, routers, plant control, building
monitoring/control, cheap Android phones - nothing that is using EMBOSS.

I would really like to get some input from *our users* here on the
Debian Med list since I need your response to draw a sensible decision.


Hi, Andreas.

The only people I know still using 32-bit software are doing BLAST etc 
on older Raspberry Pi's. However, AFAIK, the default Raspberry Pi OS 
(based on Debian Bullseye) is 32-bit even though the newer Raspberry Pi 
have 64-bit processors. Personally, I don't think it's worth the effort 
to support 32-bit software these days. I don't use EMBOSS any longer.


Bye,

  Tony.

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Re: Pique #986194 Bug closing

[Tony Travis]

On 13/12/2023 00:16, Tony Travis wrote:

On 12/12/2023 19:29, Komolehin Israel wrote:

Hi Team,

I worked on Pique package by providing autopkgtest and providing a 
patch to fix the smartpca command that blocks the upstream test from 
running successfully. CI was successful.


This closes #986194 bug.

I look forward to review and upload.


Hi, Israel.

I'm the upstream author of PIQUE: I was not aware of a problem with 
"smartpca". Have you checked the version on GitHub?



https://github.com/tony-travis/PIQUE


AFAIK, this version works correctly under Ubuntu 22.04 LTS but I've not 
tested it under Debian.


Hi, Israel.

This is the version of EIGENSOFT that I have under Ubuntu-MATE 22.04:


root@wildcat:/usr/local/src/bioinformatics/PIQUE/master/test# apt policy 
eigensoft
eigensoft:
  Installed: 7.2.1+dfsg-3build1
  Candidate: 7.2.1+dfsg-3build1
  Version table:
 *** 7.2.1+dfsg-3build1 500
500 http://gb.archive.ubuntu.com/ubuntu jammy/universe amd64 Packages
100 /var/lib/dpkg/status


PIQUE uses "smartpca" like this in the upstream test:


/usr/bin/smartpca -i sativas_GWAS.ped -a ../sativas413_recode12.map -b 
sativas_GWAS.ped -o sativas_GWAS -p sativas_GWAS -e sativas_GWAS.eval -k 5 -l 
sativas_GWAS-smartpca.log
/usr/lib/eigensoft/smartpca -p sativas_GWAS.par >sativas_GWAS-smartpca.log
ploteig -i sativas_GWAS.evec -c 1:2  -p ???  -x  -y  -o sativas_GWAS.xtxt
evec2pca-ped.perl 5 sativas_GWAS.evec sativas_GWAS.ped sativas_GWAS


I've just run the upstream tests without error under Ubuntu-MATE 22.04

As you probably know, /usr/bin/smartpca is a Perl script that creates a 
parameter file for /usr/lib/eigensoft/smartpca from its arguments.


Bye,

  Tony.

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Re: Pique #986194 Bug closing

[Tony Travis]

On 12/12/2023 19:29, Komolehin Israel wrote:

Hi Team,

I worked on Pique package by providing autopkgtest and providing a patch to fix 
the smartpca command that blocks the upstream test from running successfully. 
CI was successful.

This closes #986194 bug.

I look forward to review and upload.


Hi, Israel.

I'm the upstream author of PIQUE: I was not aware of a problem with 
"smartpca". Have you checked the version on GitHub?



https://github.com/tony-travis/PIQUE


AFAIK, this version works correctly under Ubuntu 22.04 LTS but I've not 
tested it under Debian.


Thanks for fixing the problem,

  Tony.

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Re: canu

[Tony Travis]

On 02/11/2023 10:54, George Marselis wrote:

 >  I'm just undecided because slurm itself needs
a bit more than just install the client package and you have immediate
advantage without more administration.

if I may: maybe gnu parallel would be a good suggestion, as well?


Hi, George.

GNU Parallel is a way of running 'embarrasingly' parallel jobs (i.e. 
running jobs that don't communicate with each other) concurrently. It's 
an improvement on "xargs" that also allows you to run jobs across a 
cluster of computers. This is useful when jobs consume only a small 
proportion of the available resources, but there are many jobs to run.


However, "canu" jobs typically require very large resources so "Slurm" 
is used to queue them up for execution. The problem I encountered was 
that the saved Slurm queue state was stale after an upgrade, resulting 
in a failure of "canu" to submit a job to the "Slurm" job-queue.


I didn't realise until later that "canu" will automatically use "Slurm" 
(or other resource managers like GE) if it detects that it is installed 
and, in principle, available.


I agree that GNU Parallel is good, but I wouldn't use it for "canu".

Andreas is right that "Slurm" requires non-trivial configuration before 
it can be used and, for that reason, I don't recommend adding it as a 
"suggests" to the Debian-Med "canu" package.


Bye,

  Tony.

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Re: canu

[Tony Travis]

On 01/11/2023 06:28, Andreas Tille wrote:

[...]

@Andreas, I've now removed the "canu" package and followed your advice about
installing "canu" under "bioconda3":


I *never ever* gave any advise to use bioconda.
  

https://salsa.debian.org/med-team/canu


Hi, Andreas.

I didn't say that you gave advice "to use bioconda": I said that I had 
followed your advice 'about installing "canu" under "bioconda3"'.


I needed to fix the problem we encountered with "canu" installed from 
the Debian-Med package quickly and adopted a pragmatic solution. This is 
what I read in your notes about packaging "canu" for Debian-Med:



Installing with a 'package manager' is not encouraged, but if you have no other 
choice:

Conda: conda install -c conda-forge -c bioconda -c defaults canu

Homebrew: brew install brewsci/bio/canu


At the time, I believed that had no other choice...


However, I would be interested to know if you have any plans to package it
again for Debian-Med?


Canu is and remains packaged for Debian Med.  Since you are using Ubuntu
which derives from Unstable you will not even miss it even if the package
might be removed from testing (which the bug you read is about).

In short: Please be more verbose about your problem.


Upon further investigation, it seems that the problems were caused by a 
broken "Slurm" instance on the system in question due to an upgrade (the 
saved state of the job queue was inconsistent with the new version of 
"Slurm"). I didn't know that "canu" automatically detects the presence 
of a job scheduler and will try to use it by default.


I keep forgetting that this is a Debian forum and you prefer me to send 
bug reports to the Ubuntu Bug-Tracker. I will refrain from posting about 
Debian-Med issues that I encounter under Ubuntu here in future.


Bye,

  Tony.

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canu

[Tony Travis]

Hi,

What's the status of "canu"?

The "canu" package in Debian-Med appears to be broken under Ubuntu 22.04 
and I see that it has been marked for removal in Nov 2023:



https://tracker.debian.org/pkg/canu


@Andreas, I've now removed the "canu" package and followed your advice 
about installing "canu" under "bioconda3":



https://salsa.debian.org/med-team/canu


However, I would be interested to know if you have any plans to package 
it again for Debian-Med?


Thanks,

  Tony.

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Dependency of Debian-Med packages on Apache2 web server

[Tony Travis]

Hi,

As you might remember, I have promoted the use of "x2go" for remote 
bioinformatics desktops running Debian-Med packages. However, it is 
getting increasingly difficult to obtain SSH access (used by "x2go") 
through firewalls and MFA (Multi-Factor Authentication) systems.


I'm now running "noVNC" instead, via a reverse proxy using NGINX, but 
installing "nginx" on a 'clean' install of "med-bio" under Ubuntu-MATE 
22.04 forces the removal of packages that depend on "apache2". I have 
managed to reverse-proxy to "noVNC" from Apache2, but NGINX is the 
recommended web server to reverse-proxy to "noVNC".


I realise that there are ways of running both Apache2 and NGINX on the 
same server, but I would like to know what Debian-Med "med-bio" packages 
*actually* need Apache2 because it requires quite a lot of manual 
configuration to get e.g. NGINX to use Apache2 as a reverse proxy.


I'd welcome any help or advice about NGINX and Apache2 co-existence.

Thanks,

  Tony.

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Re: Nextflow - have just used it on our HPC cluster and liked it

[Tony Travis]

On 08/05/2023 07:45, Charles Plessy wrote:

[...]  In bioconda
you have no idea whether sed is from GNU of from busybox unless you try
it or dig for a package recipe in GitHub...


Hi, Charles.

In fact, an Anaconda/Bioconda 'env' is little more than defined shell 
environment variables and a .yaml recipe to install packages from the 
Anaconda/Bioconda repo's. You can discover the version of e.g. "sed" you 
are using in an active conda 'env' by:


  which sed

If you look at the PATH in an active env you can see why:

  printenv PATH

This also reveals more: An 'env' just overloads the existing environment 
in your Linux shell and, consequently, unless you choose to install a 
different version of a program in your 'env' your PATH still results in 
the system-managed (deb) version of e.g. "sed" being run.


I run a full install of "med-bio" + Bioconda and create env's for odd 
versions of Python, Perl, R and their supporting libraries that are 
required by certain bioinformatics pipelines and that would otherwise 
conflict with the system-managed (deb) versions if installed manually.


For me, this began with QIIME which failed it's validation tests using 
the current, up-to-date, system-managed versions of supporting packages 
when Tim Booth packaged it for Bio-Linux. I used Bioconda to teach a 
course on QIIME, because Tim's Bio-Linux package gave different results 
to running QIIME on a Mac using the same data, which was a serious 
problem for my colleagues who wanted to compare their results.


As both you and Steffen have said many times, one aim of Debian-Med is 
to promote good 'reproducible' research by providing a well-defined 
environment in which to run bioinformatics pipelines. I believe the 
combination of "med-bio" + Bioconda achieves that and I have ceased my 
independent development of Bio-Linux if favour of creating a "bio-linux" 
meta-package within the Debian-Med project with help from Andreas.




I am already doing something along the lines on our HPC cluster to turn
our packages into environment modules (lmod).

https://github.com/oist/BioinfoUgrp/blob/master/DebianMedModules.md#creation-of-a-new-singularity-image

The size of the images is a bit less than 8 GiB, and I make a new image
at each point release.  Would there be some interest to make such images
in a more official way ?


I have to confess my deep ignorance of "singularity", but I am quite 
interested. I created AWS and CyVerse Bio-Linux VM's a while ago and, I 
guess, I should really bring myself up-to-date now with more modern 
approaches for HPC. On that topic, has anyone tried out QLUSTAR since 
Roland Ferrenbacher changed the licence to be 100% open source?



https://qlustar.com/


The real snag, for me, is that I can't be paid to install or support it!

However, anyone can install and use QLUSTAR themselves for free and I 
can support their use of QLUSTAR for bioinformatics. I believe it was a 
promising development when Roland Ferrenbacher agreed to support and 
endorse Debian-Med in QLUSTAR, but I've not seen much interest that 
development on our list despite Roland attending at least two Sprints.


Bye,

  Tony.

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Re: Help needed to finalise the oneTBB migration of flexbar

[Tony Travis]

On 24/01/2023 16:37, Andreas Tille wrote:

Control: tags -1 help

Hi,

I made some progress[1] in converting flexbar (which seems to be
orphaned upstream[2] so we are on our own with the migration - but the
program ist interesting anyway) but finally have hit a blocker which
you can see in the build in Salsa CI[3].

It would be great if someone could help me over this blocker.


Hi, Andreas.

Thanks very much for working on this: I had a look at the blocker, but I 
don't know enough about C++ or Tbb to help!


Sorry.

  Tony.

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Fwd: Re: Fwd: flexbar is marked for autoremoval from testing

[Tony Travis]

Hi, Knut.

I see that Johannes has now left the University. Please can you help 
Andreas resolve the issue of upgrading to use "onetbb" or give us his 
new email address?


Thanks,

  Tony.

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mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk--- Begin Message ---

On 18/12/2022 07:33, Andreas Tille wrote:

[You don't often get email from andr...@fam-tille.de. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification ]

CAUTION: External email. Ensure this message is from a trusted source before 
clicking links/attachments.


Hi Johannes,

just to let you know:  This issue


https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fseqan%2Fflexbar%2Fissues%2F38=05%7C01%7Ctony.travis%40abdn.ac.uk%7C7f79cd6d50c74f2b814708dae0ca34a7%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C638069456971458679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C=e0xqy0dVYENQuYP4uhwU%2BAc8eM0lXNf6eeJRB3Vwddg%3D=0

will keep out flexbar from next Debian stable release if not fixed soon.


Hi, Andreas.

I've just cloned the "flexbar" GitHub repo and compiled it successfully 
from source under Ubuntu-MATE 22.04 LTS + med-bio + med=bio-dev


I'm not sure what the precise relationship between Debian and Ubuntu is, 
but there are no "*onetbb*" packages available for Ubuntu 2022.04 LTS


Bye,

  Tony.


Am Wed, Jul 20, 2016 at 09:47:16AM +0200 schrieb Röhr, Johannes:

Hello Tony and Andreas,

does the mail below that I received recently mean that the Flexbar package 2.5 
will be removed because seqan (version 1.4.2) is not available?

Flexbar moved to github and in the meantime I made release 2.7 available. It 
depends on the seqan 2.1.1 release. Could you make Flexbar 2.7 available as 
debian package?

Flexbar repo and downloads:
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fseqan%2Fflexbar=05%7C01%7Ctony.travis%40abdn.ac.uk%7C7f79cd6d50c74f2b814708dae0ca34a7%7C8c2b19ad5f9c49d490773ec3cfc52b3f%7C0%7C0%7C638069456971458679%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C=6s9eCnV6%2FzyC%2Bm%2FtSbigjcbmLADoWI85UKLZ6m%2BZUHY%3D=0

Thank you and kind regards,

Johannes



Begin forwarded message:

From: Debian testing autoremoval watch 
Subject: flexbar is marked for autoremoval from testing
Date: 20 July 2016 at 06:39:17 GMT+2
To: flex...@packages.debian.org

flexbar 2.50-2 is marked for autoremoval from testing on 2016-07-31

It (build-)depends on packages with these RC bugs:
811841: seqan: FTBFS with GCC 6: no match for








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--- End Message ---

Re: [Advent bug squashing] Re: PIQUE

[Tony Travis]

On 04/12/2022 11:02, Tony Travis wrote:

[...]
You can report bugs to Debian by specifying  'bts debian' in your 
~/.reportbugrc


or by passing the -B debian option on the commandline (see reportbug(1)).


Hi, Andreas.

I've just RTFM:


ajt@beluga:~$ reportbug -B debian pique


I won't post the bug report again, but will remember for next time :-)

Bye,

  Tony.

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Re: [Advent bug squashing] Re: PIQUE

[Tony Travis]

On 04/12/2022 10:55, Andreas Tille wrote:

Hi Tony,

Am Sun, Dec 04, 2022 at 10:51:02AM + schrieb Tony Travis:

This is my BUG report:


https://bugs.launchpad.net/ubuntu/+source/pique/+bug/1998685


I filed it using "ubuntu-bug".


Well, Ubuntu bug reports do not reach our attention here.  Please use

reportbug pique

next time.


Hi, Andreas.

I can't, because it's not supported under Ubuntu/Ubuntu-MATE 22.04:


ajt@beluga:~$ reportbug pique


A GUI dialog pops up and displays:


** ERROR: "Ubuntu" BTS is currently unsupported.

Please use "ubuntu-bug" (from the apport package) for reporting bugs in Ubuntu.

You can report bugs to Debian by specifying  'bts debian' in your ~/.reportbugrc

or by passing the -B debian option on the commandline (see reportbug(1)).


Sorry about that,

  Tony.

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Re: [Advent bug squashing] Re: PIQUE

[Tony Travis]

On 04/12/2022 05:35, Andreas Tille wrote:

[...]
PS: Will you join our sprint in January?


Hi, Andreas.

Sorry, I missed your "PS" :-)

I would like to join the Debian-Med Sprint, but I'm not sure yet what my 
commitments will be in January. I'll come if I can, because I would like 
to resurrect our Debian-Med "bio-linux" package and also have a go at 
packaging the "hyb" RNA-seq pipeline I developed with Greg Kudla:



https://github.com/gkudla/hyb

Bye,

  Tony.

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Re: [Advent bug squashing] Re: PIQUE

[Tony Travis]

On 04/12/2022 05:35, Andreas Tille wrote:

Hi Tony,

Am Sun, Dec 04, 2022 at 01:39:40AM + schrieb Tony Travis:

Thanks for creating the "pique" package for my GWAS pipeline. I've just
installed it under Ubuntu 22.04 LTS and it installed quite a lot of
packages, but fails to run my tests with the error:


Error in library(multtest) : there is no package called ‘multtest’


Fixed in new upload.
  

I'll file a BUG report.


Since I want to fix a bug every day I simply take this one for today
even if not filed yet. ;-)


Hi, Andreas.

This is my BUG report:


https://bugs.launchpad.net/ubuntu/+source/pique/+bug/1998685


I filed it using "ubuntu-bug".


BTW, could you recommend some kind of test with some small example data
set?  We could wrap this into a CI test and would be able to detect
these issues immediately.


There is a Makefile in the PIQUE "test" folder on the GitHub repo that 
could be modified to test the installed version of PIQUE, rather than 
testing the version of PIQUE in the source tree.


It downloads test data: We had a conversation about this previously and 
I explained that GWAS requires quite a 'large' data-set to test it (44K 
SNP's). In fact, the 'test' data is small by comparison to a typical 
GWAS that we do with millions of SNP's. GWAS requires a genotype file 
and a phenotype file. The phenotype file, and subsets, of it are in the 
PIQUE "test" folder.


Thanks again for packaging "PIQUE",

  Tony.

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PIQUE

[Tony Travis]

Hi, Andreas.

Thanks for creating the "pique" package for my GWAS pipeline. I've just 
installed it under Ubuntu 22.04 LTS and it installed quite a lot of 
packages, but fails to run my tests with the error:



Error in library(multtest) : there is no package called ‘multtest’


I'll file a BUG report.

Bye,

  Tony.

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Re: NearVANA license

[Tony Travis]

On 18/02/2022 15:54, Tony Travis wrote:

Hi, Aymeric.

The Debian-Med community are interested in the possibility of packaging 
"NearVANA" for Debian/Ubuntu. Please will you tell us the exact license 
under which you are currently distributing "NearVANA"?

[...]


Hi, Andreas.

Aymeric sent me an email to say that he is looking into which licence to 
use for NearVANA:



This seems like good news
For the moment, all I can say is that NearVANA comes from a European project 
and will be under an open-source license. Nevertheless, there seem to be 
several different ones. I have asked the project and my institute for advice 
and I am awaiting their response.
I will tell you when I know more.


@Aymeric, please post a reply to this list when you've decided which 
licence to use. You can also ask for advice about licences here too.


Bye,

  Tony.

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PIQUE

[Tony Travis]

Hi, Lance.

I'm the upstream author of PIQUE - Is there anything I can do to help 
you to get it packaged? In particular, running the tests?


Thanks,

  Tony.
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NearVANA license

[Tony Travis]

Hi, Aymeric.

The Debian-Med community are interested in the possibility of packaging 
"NearVANA" for Debian/Ubuntu. Please will you tell us the exact license 
under which you are currently distributing "NearVANA"?


Thanks,

  Tony.

NearVANA license

[Tony Travis]

Hi, Aymeric.

The Debian-Med community are interested in the possibility of packaging 
"NearVANA" for Debian/Ubuntu. Please will you tell us the exact license 
under which you are currently distributing "NearVANA"?


Thanks,

  Tony.

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Re: Debian Med sprint from 2022-02-18 to 2021-02-20

[Tony Travis]

On 12/02/2022 13:34, Nilesh Patra wrote:

On Sat, Feb 12, 2022 at 01:27:44PM +, Tony Travis wrote:

I'd like to attend, but I don't have permission to edit the Wiki page:


https://salsa.debian.org/med-team/community/sprints/-/wikis/202202_debian-med_sprint_online


I've requested access, but have not got it yet...


Granted access to that repo, please do the needful.


Hi, Nilesh.

OK, thanks.

  Tony.

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Re: Debian Med sprint from 2022-02-18 to 2021-02-20

[Tony Travis]

On 10/02/2022 07:11, Andreas Tille wrote:

Hi,

since more people confirmed the dates Friday 2022-02-18 to Sunday
2021-02-20 the Debian Med team will do the second sprint online at
this time.  The main information about the sprint can be obtained
from the Wiki page[1].  If you have short questions you are kindly
invited to ask on our Matrix channel.

Everybody (specifically beginners) are welcome to join the fun of
our meeting.  We try to find interesting tasks also for newcomers.


Hi, Andreas.

I'd like to attend, but I don't have permission to edit the Wiki page:


https://salsa.debian.org/med-team/community/sprints/-/wikis/202202_debian-med_sprint_online


I've requested access, but have not got it yet...

I want to resume working on the Debian-Med "bio-linux" meta-package and 
tutorial, which I've neglected, and sort out the test data for "pique".


Bye,

  Tony.

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Re: [Bug 1956094] Re: deborphan guess-work removes too many files

[Tony Travis]

On 31/12/2021 21:53, Andreas Tille wrote:

[...]
Sorry, but I do not understand the problem.  What config files are you
talking about?  What is "upgrade-system"?  I'm using the command
`deborphan` itself just to learn what package might be a potential
candidate for removal.  From time to time I'm using

 apt purge `deborphan`

but well, that's users responsibility.  To learn what is really a "bug"
we need more information that this quoted mail.


Hi, Andreas.

The Debian/Ubuntu "upgrade-system" package automates updating the APT 
package list, installing updated packages and removing 'orphaned' 
packages. It is very convenient for unattended upgrades of multiple 
computers because it can either be run interactively, or without a 
controlling terminal.


The "upgrade-system" config file is:

  /etc/upgrade-system.conf

By default, "upgrade-system" allows "deborphan to 'guess' which packages 
to remove:


  ORPHANOPTS="--guess-all --libdevel"

This removes too many packages that are installed by "med-bio-dev' in 
particular, so I edited the config file to stop "deborphan" guessing:


  ORPHANOPTS="--no-guess-all --libdevel"

It appears that a recent upgrade unconditionally overwrote my edited 
"upgrade-system.conf", which resulted in most of the packages installed 
by "med-bio-dev" being removed from five of my bioinformatics servers.


Yes, it is a user's responsibility to check but I was caught out by it 
recently so I posted a bug report because I thought other people might 
also have the same problem when using "upgrade-system" with defaults.


The "upgrade-system" package is very convenient, but the default 
settings allow "deborphan" to guess what to remove. In my experience, 
that often results in "deborphan" removing packages that are needed.


Happy New Year :-)

  Tony.

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Re: [Bug 1956094] Re: deborphan guess-work removes too many files

[Tony Travis]

On 31/12/2021 12:23, Martin-Éric Racine wrote:

Those defaults work for the majority of people.

Settings can be changed as desired by editing the configuration file.

** Changed in: upgrade-system (Ubuntu)
Status: New => Won't Fix


Hi, Marin.

I *have* edited the configuration file, but the "deborphan" default has 
just caused a lot of damage on multiple systems where I use 
"upgrade-system" it appears to have overwritten my edited config files 
during a recent upgrade and, as I reported, "deborphan" removed a large 
number of packages from five of my servers where I have installed 
"med-bio" and "med-bio-dev" from the Debian-Med project. I edited the 
config file after initially running "upgrade-system" precisely because 
of this.


I'm surprised that nobody else has been bitten by this bug!

Bye,

  Tony.

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Re: autopkgtest requiring large data sets (pique, hinge)

[Tony Travis]

On 21/12/2021 21:12, Steven Robbins wrote:

On Tuesday, December 21, 2021 10:22:49 A.M. CST Nilesh Patra wrote:

On 12/21/21 9:00 PM, Pierre Gruet wrote:

On 21/12/2021 14:33, Lance Lin wrote:

Debian Medical Team,

I have started looking at adding autopkgtest suites for a variety of
packages. Two of the packages (hinge, pique) require very large data
sets to run their included examples.>>
The sizes are several GB.



I would second that. If possible, ask upstream for sensible data size that
is manageable under a few MBs.


I understand the motivation here -- it is unwieldy and unusual to have GB-
sized test data.  Irrespective of what I write below, it is always nice to
have a "small" smoke-test data set so I support asking upstream in that
spirit.

It may be the case that upstream is able to get the same code coverage out of
a smaller test data set.  Or maybe they can get a reduced-but-still-useful
coverage.

But in the days of "big data", it might be the case that testing the software
really requires a big dataset.  What are Debian's options for this?


Hi, Steve.

I'm the author of PIQUE - In fact the dataset that I use to test PIQUE 
is small in comparison to the datasets that we normally use for GWAS and 
I included a Makefile to download it, rather than including it in the repo.


Bye,

  Tony.

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Re: autopkgtest requiring large data sets (pique, hinge)

[Tony Travis]

On 21/12/2021 13:33, Lance Lin wrote:

Debian Medical Team,

I have started looking at adding autopkgtest suites for a variety of packages. 
Two of the packages (hinge, pique) require very large data sets to run their 
included examples. The sizes are several GB. It also looks like they may be 
graphical in nature.


Is it permissible for autopkgtest suites to download such large amounts of data 
from the internet? Or should they be included in the repo?

If so, I am happy to continue to look at these packages to include some basic 
level of testing.

Thank you!

As I don't have direct domain knowledge of the technology
Lance Lin 
GPG Fingerprint:  8CAD 1250 8EE0 3A41 7223  03EC 7096 F91E D75D 028F


Hi, Lance.

I'm the author of PIQUE and I included a "test" folder with a Makefile 
in it that downloads an example dataset. The data is not in the repo.


HTH,

  Tony.

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Re: Zim versus CherryTree

[Tony Travis]

On 17/11/2021 15:10, Steven Robbins wrote:

On Wednesday, November 17, 2021 4:00:30 A.M. CST Tony Travis wrote:


I use the "zim" personal Wiki for this purpose which, although it is not
ideal, is very simple to install from the Debian/Ubuntu repo's and easy
to use. I have been looking for a better alternative and was keen to try
out "Technotes". However, I have given up because it's too complicated.

May I suggest you look at "cherrytree" as an alternative to "Technotes",
because it looks quite similar and is more advanced than "Zim". It is
also available in the Debian/Ubuntu repo's. It is possible to import
notes from "Zim" into "cherrytree" and I am evaluating it for my own


Hello!  I have also long been using Zim for informal note taking.  It is
adequate but if there's something better, I'd be keen to hear about it.  Maybe
you (or anyone!) would post your experience comparing the two?


Hi, Steve.

I'm still undecided about CherryTree because it doesn't import all the 
Zim Wiki markup properly. In particular it does not import URL's and 
only seems to import text formatting (e.g. bold and italics). I also 
find the user interface quite clumsy in comparison to Zim. For example, 
when I select 'bold' text, the toolbar icon does not indicate that bold 
text is selected as it does in Zim. This is not a show-stopper, of 
course, but after trying quite hard to move over to CherryTree I find 
myself back using Zim again because it is so easy to use and mostly does 
everything that I want, but with the notable exception of not allowing 
me to sort search results by date. Zim's multi-page support is also 
lack-lustre when e.g. trying to move items from one page to another with 
both pages open in separate windows - Zim makes one window read-only!


Please post here any good Zim alternatives that you discover.

Thanks,

  Tony.

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Re: Project proposal for the Debian Med group

[Tony Travis]

On 17/11/2021 08:49, Guido Rovera wrote:

Dear Debian Med members,
I hope this email finds you well, and that your projects are running 
smoothly.
Since I haven't heard back from you, I would like to know if there is 
anyone interested in the "TechneNotes" project 
(https://grovera.gitlab.io/technenotes/ 
)

[...]


Hi, Guido.
I cloned the GitHub repo and tried to install the software when you 
posted your previous message, but I found it very difficult to build and 
install (there is no .deb package available AFAIK). It is not by any 
means a 'simple' solution to the problem of documenting your own work.


I use the "zim" personal Wiki for this purpose which, although it is not 
ideal, is very simple to install from the Debian/Ubuntu repo's and easy 
to use. I have been looking for a better alternative and was keen to try 
out "Technotes". However, I have given up because it's too complicated.


May I suggest you look at "cherrytree" as an alternative to "Technotes", 
because it looks quite similar and is more advanced than "Zim". It is 
also available in the Debian/Ubuntu repo's. It is possible to import 
notes from "Zim" into "cherrytree" and I am evaluating it for my own 
work. This is the "cherrytree" website:



https://www.giuspen.com/cherrytree/


Also have a look at some alternatives to "cherrytree":


https://alternativeto.net/software/cherrytree/


HTH,

  Tony.

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Re: Any volunteer to verify autopkgtest of spades?

[Tony Travis]

On 26/09/2021 00:12, tony mancill wrote:

Hi Tony,

In case it helps, here are the commands I used to build the latest
spades package and run the autopkgtest against the resulting binary.
[...]
I hope that helps.


Hi, Tony.

Thanks, it helped me a lot!

  Tony.

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Re: Any volunteer to verify autopkgtest of spades?

[Tony Travis]

On 23/09/2021 21:26, Pierre Gruet wrote:

[...]
No problem!
You could install git-buildpackage if you don't have it, and then type
 gbp clone https://salsa.debian.org/med-team/spades.git
to get all the relevant branches from Salsa. If you have a ssh key 
properly set up for Salsa,

 gbp clone git:salsa.debian.org:med-team/spades
also works.


Hi, Pierre.

AFAIK, I only have guest access to "salsa", but I've cloned it.

If you don't know git-buildpackage, you could refer to the pdf provided 
by the package debmake-doc [0] and also to the documentation of 
git-buildpackage [1], which is nice.


I don't know it and I will read the doc's :-)


Alternatively, just using
 git clone https://salsa.debian.org/med-team/spades.git
would be enough.

If you need more details, just ask.


OK and thanks for your help getting me started,

  Tony.

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Re: Any volunteer to verify autopkgtest of spades?

[Tony Travis]

On 23/09/2021 17:16, Steffen Möller wrote:

[...]
You would install both the source tree (with the Debian folder) and
install the binary. Then run

sh debian/tests/run-unit-test

from the source directory.


Hi, Steffen.

Please forgive my ignorance, but I don't know where to git clone a copy 
of the source tree from. Any advice would be gratefully accepted :-)


Thanks,

  Tony.

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Re: Any volunteer to verify autopkgtest of spades?

[Tony Travis]

On 23/09/2021 13:53, Andreas Tille wrote:

Hi,

some time ago I've pushed a packaging update for Spades.  Unfortunately
the autopkgtest fails with
[...]


Hi, Andreas.

I'm willing to volunteer, but I don't know how to run "autopkgtest": Can 
I just download your package and test it?


Bye,

  Tony.

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Re: q2-diversity tests Re: report on first qiime tutorial with Debian packages

[Tony Travis]

On 12/08/2021 19:16, Steffen Möller wrote:

--
Ran 153 tests in 557.862s


Hi, Steffen.

QIIME/QIIME2 are notoriously sensitive to the versions of supporting 
programs so I think it is important to validate your packaging of QIIME2 
against the same analysis using the upstream-supported Bioconda package.


I've taught QIIME2 using Jupyter Notebooks on Cyverse:


https://cyverse-jupyter-qiime2.readthedocs-hosted.com/en/latest/README.html


This was well received by the course participants in comparison to when 
they were just using the CLI.


HTH,

  Tony.

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Re: Help request - How to install qiime plugins which are not available in Debian?

[Tony Travis]

On 18/07/2021 14:29, Andreas Tille wrote:

[...]
It would help if you check the list of plugins you need (or any other
software you might need) and tell us here.  If users are (silently)
using other systems (like the suggested BioConda) we do not get any
response what to do to make Debian Med better.  I have no problems
with other systems - as long as users simply tell us what is missing
here or what bugs are affecting their work.


Hi, Andreas.

QIIME is particularly sensitive to the versions of supporting software 
that it uses and I gave up trying to validate the APT-managed version 
that Tim Booth created for Bio-Linux. The reason I run QIIME under 
Bioconda is that I can install precisely the validated version of all 
the supporting software without any conflicts with the underlying 
system-managed packages. Validation of QIIME is particularly important 
when comparing results obtained by other people on different platforms.


Bye,

  Tony.

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Re: Help request - How to install qiime plugins which are not available in Debian?

[Tony Travis]

On 18/07/2021 14:19, Beatrice Torracca wrote:

[...]
Is the qiime installation via bioconda going to clash with the qiime
from the Debian testing repository I installed via apt?


Hi, Beatrice.

No, Bioconda provides a separate isolated environment in which to run 
QIIME. The advantage is that you can still use APT-managed packages from 
within a Bioconda environment, but anything you install within Bioconda 
is stored separately to the APT-managed packages and accessed using a 
PATH that prioritises Bioconda versions over APT-managed versions.


In a very real sense, you get the best of both worlds. However, there is 
one catch: Don't allow the "miniconda" bootstrap to 'initialise' your 
shell or it *will* conflict with APT-managed packages by prioritising 
Bioconda versions over Ubuntu/Debian-Med versions. You can solve this by 
using my Bioconda 'wrapper'.


HTH,

  Tony.

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bioconda_wrapper.tgz
Description: application/compressed-tar

Re: Help request - How to install qiime plugins which are not available in Debian?

[Tony Travis]

On 18/07/2021 07:57, Beatrice Torracca wrote:

[...]
I guess otherwise I would have to go the virtualbox route, which is
also kinda blurry to me (I imagine any VM, like QEMU, would do,
right?). So, any pointers to talks/presentations/tutorial on qiime in
Debian would be much appreciated.


Hi, Beatrice.

I recommend using QIIME2 under Bioconda:


https://docs.qiime2.org/2021.4/install/native/


You can also follow the QIIME2 tutorials:


https://docs.qiime2.org/2021.4/tutorials/


In particular, I recommend the 'Moving Pictures' tutorial:


https://docs.qiime2.org/2021.4/tutorials/


HTH,

  Tony.

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Re: Meta: We should think more about the Windows Subsystem for Linux

[Tony Travis]

On 20/06/2021 12:41, Steffen Möller wrote:

[...]
Anyway, there is something. And yes, we are too quiet about it, even if
it feels much like MS is embracing us again, but it is better than what
we have. And I wish we would have the same for the mac. Well, we do, it
is called conda/brew/guix, but I mean without a recompilation. Once we
have identified a series of core workflows that Debian Med supports, I
suggest to have these tested in routine also with WSL.


Hi, Steffen.

[WSL] Been there, done that, got the T-shirt :-)

I'm up for volunteering to test "med-bio" on WSL.

Bye,

  Tony.

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Honourable Mention

[Tony Travis]

Hi,

I just got an email from Daniel Barker, who gave Debian-Med an 
honourable mention on page 30 in issue 16 of "Hello World" magazine in 
an article about bringing bioinformatics to schools:



https://helloworld.raspberrypi.org/issues/16


Thanks,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages) [correction]

[Tony Travis]

On 26/05/2021 16:41, Tony Travis wrote:

[...]
I will also be giving due credit to Debian-Med for packaging all the 
software I'm now using as "Bio-Linux" = Ubuntu-MATE 20.04 + med-bio.


Hi, Debian-Med Team.

I gave due credit for your hard work packaging bioinformatics software 
today in my talk during the first day of the SANH (South Asia Nitrogen 
Hub) Workshop that I'm running online from home this week.


Thanks,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages) [correction]

[Tony Travis]

On 23/07/2020 22:31, Tony Travis wrote:

[...]

I just want to make sure you will not create the false impression to
naive users that installing med-* is needed to just run pique (which
meanwhile was accepted in unstable).


I am encouraging former Bio-Linux 8.0.8 users to upgrade to Ubuntu-MATE 
20.04 LTS and install "med-bio" and "med-bio-dev", but not just to run 
PIQUE :-)


Hi, Andreas.

I've updated PIQUE recently to use PLINK 1.9, and fixed some bugs, prior 
to using it for an upcoming bioinformatics workshop from 7-11 June.


Please will you let me know what I need to do now to get the package you 
created accepted and available to install under Ubuntu 18.04/20.04 LTS?


I will also be giving due credit to Debian-Med for packaging all the 
software I'm now using as "Bio-Linux" = Ubuntu-MATE 20.04 + med-bio.


Bye,

  Tony.

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Re: Outreachy project: complete workflows of tools

[Tony Travis]

On 07/03/2021 23:47, Tassia Camoes Araujo wrote:

Hi all,

On 2021-03-05 11:09, Tassia Camoes Araujo wrote:

[...]
Since deadline is approaching quickly, I suggest we move this off-list
and start writing in a wiki or pad.


Here is my first draft, pasted below for your reference, but you can
edit the text directly in this pad:
https://storm.debian.net/shared/OCYsOOEqJ5-CcfjVxIiye-ex-4LheegyP1pkIFghMKa

Help needed to write the Intern tasks section. Also, please check if you
have better scientific articles to recommend and list a few tools to be
used in the starter tasks.

Please help shaping this proposal so it ***really*** makes sense and
attract interns ;-)


Hi, Tassia.

I recommend using "flexbar", which I use, instead of "Trimmomatic":


https://github.com/seqan/flexbar


Also, depending on the sequencing technology used, consider assembling 
short-paired-end reads with e.g. Pear:



https://github.com/tseemann/PEAR


HTH,

  Tony.

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Re: Outreachy project: complete workflows of tools

[Tony Travis]

On 04/03/2021 16:54, Andreas Tille wrote:

[...]
If I understood you correctly your question to Tony was whether he might
like to volunteer to support drafting an Outreachy proposal.  Guessing
from Tony's response to your mail this was not totally clear to him.


Hi, Andreas.

You're right, I was just suggesting that the Bio-Linux documentation and 
the "Introduction to Bio-Linux" tutorial I helped Tim Booth to create in 
particular might be a useful starting point for an 'Outreachy' projeect.


I'm planning to re-write the tutorial, which includes QIIME, for my 
Debian-Med version of Bio-Linux, but it would be really helpful if 
someone is interested in doing that as part of an 'Outreachy' project.


Sorry, I misunderstood Tássia's email.

  Tony.

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Re: Outreachy project: complete workflows of tools

[Tony Travis]

On 03/03/2021 23:21, Tassia Camoes Araujo wrote:

[...]
Reading the list archive I saw a message by Tony Travis as a great
example of solving biological problems with our tools: "I use the
software you've packaged for my own work on the molecular genetics of
drought-tolerance and Nitrogen-use-efficiency in Rice and for studies of
the micro-virome of Tsetse files and Mosquitoes as well as for the
cancer genomics work on the cluster at the Mario Negri Institute in
Milan."


Hi, Tassia.

I've worked with the Debian-Med team for many years, starting with my 
contribution to the Bio-Linux project:



http://environmentalomics.org/bio-linux/


I'm now 'last man standing' on the Bio-Linux project, which is now 
entirely supported by the Debian-Med team. I install 'Bio-Linux' from a 
customised Ubuntu-MATE 20.04 LTS 'live' USB-stick with "med-bio" and 
"med-bio-dev" plus "x2goserver" and Bioconda.


One of the most important aspects of the Bio-Linux project was good 
documentation and tutorials about the software included. We used 
Bio-Linux 'live' instances booted from USB-sticks or VM's to teach 
bioinformatics tutorial courses and I continue to do this from time to 
time. In particular, I am currently employed part-time on a UK/India 
SANH project at the University of Aberdeen to teach GWAS and other 
methods and I'm helping researchers in India install "med-bio" from 
Debian-Med under Ubuntu-MATE 20.04 LTS on their computers for GWAS.


Thanks for your interest!

  Tony.

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Re: Organising Debian Med Sprint starting on Thursday

[Tony Travis]

On 16/02/2021 17:06, Andreas Tille wrote:

Hi friends of Debian Med,

this will be our first online sprint.  I will miss you all in person but
lets make the best out of it - hopefully meeting people who never made
it to any sprint due to the big effort to travel.
[...]

Hi, Andreas.

I won't be attending the Sprint, but do I want to thank you and everyone 
else contributing to Debian-Med for all your hard work and dedication.


I now install "med-bio" and "med-bio-dev" under Ubuntu-MATE 20.04 LTS 
along with "x2go" and "Bioconda" as "Bio-Linux". I use the software 
you've packaged for my own work on the molecular genetics of 
drought-tolerance and Nitrogen-use-efficiency in Rice and for studies of 
the micro-virome of Tsetse files and Mosquitoes as well as for the 
cancer genomics work on the cluster at the Mario Negri Institute in Milan.


I also recommend Debian-Med to anyone who wants to do bioinformatics: 
Most recently, I did a remote installation of 'Bio-Linux' on a computer 
in India as part of my work at the University of Aberdeen in Scotland.


Thanks for making all this useful software so easy to install,

  Tony.

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EIGENSOFT

[Tony Travis]

Hi,

I still struggle to know the best way to report errors I find running 
Debian-Med packages under Ubuntu, so I'm just going to report it here.


There is an absolute path to "fixgreen" in the "ploteig" script in the 
"eigensoft" package. Sorry I'm not a true Debianista and before I get 
told off the Debian reporting tools don't work under Ubuntu. I obtained 
a copy of "fixgreen" from the EIG5.0.2.tgz distribution tarball.


Thanks again for all your hard work maintaining Debian-Med,

  Tony.

root@wildcat:/usr/local/src/bioinformatics/EIGENSOFT/EIG-6.1.4/bin# diff 
-Naur ploteig /usr/bin/ploteig

--- ploteig 2016-09-07 16:00:02.0 +0100
+++ /usr/bin/ploteig2021-01-21 19:24:39.535788738 +
@@ -1,4 +1,8 @@
-#!/usr/local/bin/perl  -w
+#!/usr/bin/perl  -w
+#@(#)ploteig  2021-01-21  last modified by A.J.Travis
+#
+# Removed absolute path to "fixgreen"
+#

 ### ploteig -i eigfile -p pops -c a:b [-t title] [-s stem] [-o 
outfile] [-x] [-k]  [-y] [-z sep] -r colorstring -m xmul -n ymul

 use Getopt::Std ;
@@ -135,7 +139,7 @@
   $psfile  =~ s/xtxt/ps/ ;
  }
 system "gnuplot < $gnfile > $psfile" ;
-system "/home/np29/bin/fixgreen  $psfile" ;
+system "fixgreen  $psfile" ;
 system "ps2pdf  $psfile " ;
 }
 unlink (@T) unless $keepflag ;


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metaphlan2-data

[Tony Travis]

Hi,

During routine checking, I noticed that a file is missing from 
"metaphlan2-data" in "med-bio":



debsums -ac metaphlan2-data
debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from 
metaphlan2-data package)


The file is present in the metaphlan2-data.deb:


apt download metaphlan2-data
dpkg-deb -Rv metaphlan2-data_2.6.0+ds-3_all.deb metaphlan2-data_2.6.0+ds-3_all
./
./usr/
./usr/sbin/
./usr/sbin/metaphlan2-data-convert
./usr/share/
./usr/share/doc/
./usr/share/doc/metaphlan2-data/
./usr/share/doc/metaphlan2-data/changelog.Debian.gz
./usr/share/doc/metaphlan2-data/copyright
./usr/share/man/
./usr/share/man/man8/
./usr/share/man/man8/metaphlan2-data-convert.8.gz
./var/
./var/lib/
./var/lib/metaphlan2-data/
./var/lib/metaphlan2-data/bt2.md5
./var/lib/metaphlan2-data/markers.fasta
ls -l metaphlan2-data_2.6.0+ds-3_all/var/lib/metaphlan2-data/markers.fasta
-rw-r--r-- 1 root root 771154614 Sep  6  2016 
metaphlan2-data_2.6.0+ds-3_all/var/lib/metaphlan2-data/markers.fasta


The manifest has an entry for "markers.fasta", which is why debsums 
reports it as a missing file:



fgrep markers.fasta metaphlan2-data_2.6.0+ds-3_all/DEBIAN/md5sums
3f824117b27a052ede59c68c2f1dead4  var/lib/metaphlan2-data/markers.fasta


However, "markers.fasta" is not installed.

I copied the file into place manually because I can't work out why it 
isn't installed with the rest of the package?


Any ideas/explanations about why would be apreciated :-)

Thanks,

  Tony.

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metaphlan2-data

[Tony Travis]

Hi,

During routine checking, I noticed that a file is missing from 
"metaphlan2-data" in "med-bio":



debsums -ac metaphlan2-data
debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from 
metaphlan2-data package)


The file is present in the metaphlan2-data.deb:


apt download metaphlan2-data
dpkg-deb -Rv metaphlan2-data_2.6.0+ds-3_all.deb metaphlan2-data_2.6.0+ds-3_all
./
./usr/
./usr/sbin/
./usr/sbin/metaphlan2-data-convert
./usr/share/
./usr/share/doc/
./usr/share/doc/metaphlan2-data/
./usr/share/doc/metaphlan2-data/changelog.Debian.gz
./usr/share/doc/metaphlan2-data/copyright
./usr/share/man/
./usr/share/man/man8/
./usr/share/man/man8/metaphlan2-data-convert.8.gz
./var/
./var/lib/
./var/lib/metaphlan2-data/
./var/lib/metaphlan2-data/bt2.md5
./var/lib/metaphlan2-data/markers.fasta
ls -l metaphlan2-data_2.6.0+ds-3_all/var/lib/metaphlan2-data/markers.fasta
-rw-r--r-- 1 root root 771154614 Sep  6  2016 
metaphlan2-data_2.6.0+ds-3_all/var/lib/metaphlan2-data/markers.fasta


The manifest has an entry for "markers.fasta", which is why debsums 
reports it as a missing file:



fgrep markers.fasta metaphlan2-data_2.6.0+ds-3_all/DEBIAN/md5sums
3f824117b27a052ede59c68c2f1dead4  var/lib/metaphlan2-data/markers.fasta


However, "markers.fasta" is not installed.

I copied the file into place manually because I can't work out why it 
isn't installed with the rest of the package?


Any ideas/explanations about why would be apreciated :-)

Thanks,

  Tony.

Fwd: Re: [qiime2/qiime2] InternalDirectory's rename() will fail on python 3.8 (#520)

[Tony Travis]

Hi,

I've received this email from GitHub about QIIME development that may be 
of interest to us packaging QIIME for Debian-Med.


Please join the conversation on GitHub if you're interested.

Thanks,

  Tony.

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--- Begin Message ---
Hello,

I've been working on a targeted patch set which covers at least the test suite 
for python versions 3.8 and 3.9.  The patches are available here after for the 
moment, but I can ready a proper merge request in the coming week, if you deem 
this more convenient:

https://salsa.debian.org/med-team/qiime/-/blob/master/debian/patches/python3.8.patch

https://salsa.debian.org/med-team/qiime/-/blob/master/debian/patches/python3.9.patch

Please be aware that I do not have a python 3.7 installation readily available 
at the moment, so couldn't make sure at 100% that the changes were non 
breaking; semantically they shouldn't hurt, hopefully.

Kind Regards,
Étienne.

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You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:
https://github.com/qiime2/qiime2/issues/520#issuecomment-736096696--- End Message ---

Re: armhf regressions in a few packages

[Tony Travis]

On 22/11/2020 06:51, Michael R. Crusoe wrote:

[...]
For bioinformatics, there is no reason to support armhf.


Hi, Michael.

I think there is, at least for use in education e.g.:


https://open.ed.ac.uk/4273%CF%80-bioinformatics-on-the-raspberry-pi/


I'm currently running Ubunu-MATE 20.04.1 on an arm64 Pinebook Pro and 
Rockpro64 which, admittedly, are arm64 not armhf :-)


Bye,

  Tony.

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Re: ORCA

[Tony Travis]

On 03/11/2020 07:06, Andreas Tille wrote:

Hi Steffen,

On Tue, Nov 03, 2020 at 01:36:00AM +0100, Steffen Möller wrote:

I had a second look. Impressive. Seems like linuxbrew has evolved
enormously.


If you had a look could you please give a short summary?  For me it
sounds like another packaging system (like Conda).  Would you mind doing
some comparison?  Would anybody consider contacting ORCA developers and
invite them to join our list?  I'm wondering whether a docker container
featuring Debian Med packages might have advantages or disadvantages and
I'm keen on learning what those disadvantages might be.


Hi, Andreas.

OK, I'm willing to volunteer to contact them!

I've been using Docker a lot recently to run virus scanning pipelines 
and I have very mixed feelings about it. It's good if you understand how 
to use it, but presents huge opportunities to get it wrong and can be 
quite impenetrable if you don't know or have to motivation to use it 
properly. On balance, I think it is better to use Bioconda instead.


Bye,

  Tony.

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ORCA

[Tony Travis]

Hi,

Has anyone looked at ORCA?


https://academic.oup.com/bioinformatics/article/35/21/4448/5475597


It has recently been promoted on Cyverse-UK:


https://cyverseuk.org/


Came to my attention because of the reference to Bio-Linux, which I've 
used a lot on the University of Arizona iPlant/Cyverse training cluster.


Bye,

  Tony.

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mafft [was Re: VIP]

[Tony Travis]

On 08/07/2020 14:56, Michael Crusoe wrote:

[...]
Could be that mafft has reached a point in the computation that is still 
single threaded.


Their script specifies 8 threads: 
https://github.com/keylabivdc/VIP/blob/d69b5e7615d8da76ef0dd66e51867c8ec42588d4/MSA.sh#L28


Though that is a different script than in the container, where it 
references `--thread $total_cores` where `total_cores` appears to be set 
to half of your available cores. Which matches your 12 of 24 cores report.


You could replace that `--threads $total_cores` with `--threads -1` to 
see if that helps.


Hi, Michael.
I've been struggling to find out what the problem is for some time now 
and I've tried the version of "mafft" packaged by you for Debian-Med.


The problem is not with "mafft", which is a shell script, but with the 
"disttbfast" program spawned by "mafft", which hangs at 100% CPU on one 
thread for more than seven days without completing and returning control 
back to "mafft" regardless of how many threads are actually specified.


This only seems to happen with certain viral sequences and might be 
because "disttbfast gets stuck in a local minimum and never converges?


I've just posted a bug-report including a 'problem' sequence to the 
Ubuntu bug-tracker that should, presumably, find its way to you as the 
Debian "mafft" package maintainer.


Thanks for looking into my VIP "mafft" problem,

  Tony.

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Re: VIP

[Tony Travis]

On 25/08/2020 00:17, Steffen Möller wrote:

[...]
https://tracker.debian.org/pkg/centrifuge

was only very recently added to the distribution. I _very_ much support
ourselves shifting our discussions from packaging towards using our
packages. @Tony, if you have any more or less public dataset in mind
that we all could work along with then this would possibly be helpful.


Hi, Steffen.

The sequences I'm analysing right now for the IAEA are unpublished data 
and are _very_ large, which is part of the problem for VIP. However, the 
VIP-0.2.0 docker image contains test data that can be extracted from it:



docker pull yang4li/vip-docker


I used this test data to debug my VIP 0.2.1 Bioconda env

Thanks for supporting discussions about using Debian-med packages. One 
of the most important aspects of Bio-Linux was the effort that we put 
into documenting and supporting the software. I believe that this is 
also important for Debian-Med to be more widely used by biologists.


My revised notion of 'Bio-Linux' is a simple to deploy platform for use 
by biologists based on Ubuntu-MATE with "med-bio" amd "x2go-server" 
pre-installed. I can already create bootable 'live' install DVDs. All I 
need to do now is write the documentation and tutorials :-)


  Tony.

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Re: VIP

[Tony Travis]

On 08/07/2020 18:01, Tony Travis wrote:

On 08/07/2020 14:56, Michael Crusoe wrote:

[...]
Perhaps try the author's vip2 container? 
https://hub.docker.com/r/yang4li/vip2 Though I can find no source for 
either container, so it is a bit risky.


Hi, Michael.

OK, I've pulled the vip2 container and I'm having a look at it now...

Interestingly it uses "miniconda3" under Ubuntu 18.04, which is how I 
have been running it without a Docker container. However, there is no 
documentation about how to build the necessary databases.


Hi, Michael.

The VIP2 container has a binary in it to replace the VIP.sh script, but 
no source code and no information about how to create the databases it 
requires. Unlike the VIP-0.2.0 container on GitHub there are no 
pre-existing databases we can use in the VIP2 container.


I've had partial success running VIP-0.2.0, which I extracted from the 
docker image and created a Bioconda env: The GitHub repo only contains 
VIP-0.1.1, which has been cloned and modified to create VIP-0.2.0 in the 
docker image, but these changes have not been committed and pushed back 
into the GitHub repo. The VIP project appears to have been abandoned...


Only three of six jobs I started over a week ago have finished and I'm 
looking for an alternative virus identification pipeline that can do the 
analysis better/faster.


The VIP2 container appears to run "Centrifuge", so I was interested to 
see the messages about "Centrifuge" here and I would welcome help/advice 
from anyone who has used "Centrifuge" to detect viruses in a microbiome.


Thanks,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages) [correction]

[Tony Travis]

On 23/07/2020 13:37, Andreas Tille wrote:

[...]

The "pique-input" script should be running /usr/lib/eigensoft/smartpca, not
/usr/bin/smartpca and my version does:


I'll check this.  However, in principle I do not consider it the best
idea to use some program that is private to eigensoft and ignore the
available user interface in /usr/bin.


Hi, Andreas.

The EIGENSOFT "smartpca.perl" wrapper creates a parameter file for input 
to "/usr/lib/eigensoft/smartpca" in a similar way that I did using a 
subroutine in my "pique-input" script. However, I've changed my script 
to use the public wrapper "/usr/bin/smartpca" as you suggest.



[...]
For Debian we usually trust *released* version (if available) so
if you would please tag what should be packaged I could package
your tagged release.


OK, I want to make some further changes before tagging a new release but 
I've already pushed my changes to: https://github.com/tony-travis/PIQUE



[...]
I just want to make sure you will not create the false impression to
naive users that installing med-* is needed to just run pique (which
meanwhile was accepted in unstable).


I am encouraging former Bio-Linux 8.0.8 users to upgrade to Ubuntu-MATE 
20.04 LTS and install "med-bio" and "med-bio-dev", but not just to run 
PIQUE :-)



[...]

It's not possible to test PIQUE without a data-set large enough to use for
GWAS, which is why I use "wget" to download one and avoid storing large blob
in the GitHub repo. The data-sets we normally use contain millions of SNPS,
but this small data-set is what we used during the development of PIQUE and
what we use when teaching how to use it.

Not sure if that helps?


The information itself helps.  As far as I know its permitted in autopkgtest
to download data - so if we know there is no better way than we can try
this.


Thanks,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages) [correction]

[Tony Travis]

On 23/07/2020 07:56, Andreas Tille wrote:

Hi Tony,

On Wed, Jul 22, 2020 at 11:46:03PM +0100, Tony Travis wrote:

Analysis finished: Mon Jul 20 13:56:47 2020

Create sativas_GWAS.covar file...
smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
OOPS -i flag not specified at /usr/bin/smartpca line 21.
pique: error - Can't read sativas_GWAS.evec
make: *** [Makefile:29: input] Fehler 255


Hi, Andreas.

The "pique-input" script should be running /usr/lib/eigensoft/smartpca, 
not /usr/bin/smartpca and my version does:



root@beluga:/opt/local/src/GWAS/PIQUE/test# make |& tee make.log
[...] > root@beluga:/opt/local/src/GWAS/PIQUE/test# fgrep smartpca *.log
make.log:/usr/lib/eigensoft/smartpca -p sativas_GWAS.par > 
sativas_GWAS-smartpca.log
sativas_GWAS-pique-input.log:/usr/lib/eigensoft/smartpca -p sativas_GWAS.par


Please will you try a "git pull" to make sure your copy of my PIQUE 
GitHub repo is up-to-date - Thanks.



[...]
libparallel-forkmanager-perl is in the list of Depends of the pique
package uploaded to new - so this should be settled.


Yes, I understand that - I'm just letting you know that all the other 
dependencies of PIQUE are already satisfied by installing the "med-bio" 
and "med-bio-dev" meta-packages, which is a vast improvement over the 
way we used to install it in the bad old days :-)hadhad



I'll update PIQUE on Github and remove the tar-ball dependencies from it now
that everything I need is available in "med-bio" or "med-bio-dev".


Well, "everything you need" is (hopefully) specified as Depends of the
pique package - if not that should be fixed.  IMHO we need to sort out
the details of the error above.  Could you please check with a recent
version of eigensoft the issue behing the

OOPS -i flag not specified at /usr/bin/smartpca line 21.

message?  The version that was used in this test is 7.2.1+dfsg-1.


See above, "pique-input" should run "/usr/lib/eigensoft/smartpca".


root@beluga:/opt/local/src/GWAS/PIQUE/test# apt policy eigensoft
eigensoft:
  Installed: 7.2.1+dfsg-1build1
  Candidate: 7.2.1+dfsg-1build1
  Version table:
 *** 7.2.1+dfsg-1build1 500
500 http://gb.archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages
100 /var/lib/dpkg/status



[...]
Regarding testing I'd like to refresh my mail from March of last
year which I somehow can not find inside the web archive, so
I'm copying its content here:


Regarding testing pique (and to find such missing depends):  test/Makefile
also uses wget to download data.  Could you provide a simple shell script
that is using only the available data to test the functionality of pique

   a) in a build time test

   b) as autopkgtest


It's not possible to test PIQUE without a data-set large enough to use 
for GWAS, which is why I use "wget" to download one and avoid storing 
large blob in the GitHub repo. The data-sets we normally use contain 
millions of SNPS, but this small data-set is what we used during the 
development of PIQUE and what we use when teaching how to use it.


Not sure if that helps?

Thanks again,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages) [correction]

[Tony Travis]

On 20/07/2020 13:03, Andreas Tille wrote:

[...]
OK, just ITPed package.  BTW, I was running make in the tests dir and
it ends with:


Analysis finished: Mon Jul 20 13:56:47 2020

Create sativas_GWAS.covar file...
smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
OOPS -i flag not specified at /usr/bin/smartpca line 21.
pique: error - Can't read sativas_GWAS.evec
make: *** [Makefile:29: input] Fehler 255


Hi, Andreas.

I created a pristine Ubuntu-MATE 20.04 VM, installed "med-bio" and 
"med-bio-dev" into it, then installed PIQUE from GitHub without any 
tar-ball dependencies. The only missing dependency was 
"libparallel-forkmanager-perl", which I installed, and then the PIQUE 
test ran without error.


Sorry that PIQUE has become so out-of-date and unmaintained. We do use 
it a lot under Ubuntu-MATE 18.04, but I'm now upgrading to 20.04 LTS.


I'll update PIQUE on Github and remove the tar-ball dependencies from it 
now that everything I need is available in "med-bio" or "med-bio-dev".


Thanks again for your work packaging PIQUE,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages) [correction]

[Tony Travis]

On 20/07/2020 10:46, Tony Travis wrote:

[...]
PIQUE is a software pipeline for performing genome wide association 
studies (GWAS). The main function of PIQUE is to provide ‘convenience’ 
wrappers that allow users to perform GWAS using the popular program 
EMMAX (Kang et al., 2010) without the need to be familiar with all of 
the software tools used to generate the required EMMAX input files. 
PIQUE will also perform a number of of quality control steps prior to 
running EMMAX, ensuring that the various input data files are in the 
correct format. PIQUE proceeds in two main stages although there are 
multiple entry and exit points from which the pipeline can be run. The 
first stage consists of running the “emmax-input” program, which can 
read genotype and phenotype information in several different formats and 
generates all the necessary input files required to run EMMAX. The 
second step in the pipeline uses the “emmax-run” program to actually run 
EMMAX using the files generated by “emmax-input” (or pre-existing 
user-supplied input files) to perform the GWAS and output the analysis 
summary files.


Hi, Andreas.

Please replace "emmax-input" and "emmax-run" with "pique-input" and 
"pique-run".


Thanks,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages)

[Tony Travis]

On 03/07/2019 09:18, Tony Travis wrote:

On 02/07/2019 15:08, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 04:15:11PM +0100, Tony Travis wrote:

    2. Is there any description of PIQUE that could be used as long
   description for the package.  I've checked doc/pique_manual.odt
   but despite its filename it says it is the ParSNP manual
   (btw, parsnp is packaged) and doc/pique_tutorial.odt does
   also not contain anything that would enlighten me about PIQUE
   at first sight.
   Feel free to simply replace the FIXME in

https://salsa.debian.org/med-team/pique/blob/master/debian/control


Yes, I'll sort that out: We called it "ParSNP" at first, but I 
subsequently

discovered that someone has already used that name!


I've stumbled upon old mails.  Emmax is in new queue since some time but
final PIQUE packaging is just blocked due to missing long description.


Hi, Andreas.

OK, I'll sort that out.


Hi, Andreas.

Sorry, I really must apologise for taking so long to do this:

PIQUE is a software pipeline for performing genome wide association 
studies (GWAS). The main function of PIQUE is to provide ‘convenience’ 
wrappers that allow users to perform GWAS using the popular program 
EMMAX (Kang et al., 2010) without the need to be familiar with all of 
the software tools used to generate the required EMMAX input files. 
PIQUE will also perform a number of of quality control steps prior to 
running EMMAX, ensuring that the various input data files are in the 
correct format. PIQUE proceeds in two main stages although there are 
multiple entry and exit points from which the pipeline can be run. The 
first stage consists of running the “emmax-input” program, which can 
read genotype and phenotype information in several different formats and 
generates all the necessary input files required to run EMMAX. The 
second step in the pipeline uses the “emmax-run” program to actually run 
EMMAX using the files generated by “emmax-input” (or pre-existing 
user-supplied input files) to perform the GWAS and output the analysis 
summary files.


I'll update my PIQUE GitHub repository with the new documents ASAP:


https://github.com/tony-travis/PIQUE.git


Thanks again,

  Tony.

--
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Re: VIP

[Tony Travis]

On 08/07/2020 14:56, Michael Crusoe wrote:

[...]
Perhaps try the author's vip2 container? 
https://hub.docker.com/r/yang4li/vip2 Though I can find no source for 
either container, so it is a bit risky.


Hi, Michael.

OK, I've pulled the vip2 container and I'm having a look at it now...

Interestingly it uses "miniconda3" under Ubuntu 18.04, which is how I 
have been running it without a Docker container. However, there is no 
documentation about how to build the necessary databases.


Thanks again for your help,

  Tony.

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Re: VIP

[Tony Travis]

On 08/07/2020 14:56, Michael Crusoe wrote:

[...]
Perhaps try the author's vip2 container? 
https://hub.docker.com/r/yang4li/vip2 Though I can find no source for 
either container, so it is a bit risky.


The yang4li/vip-docker container uses a very old version of mafft, from 
2013.


Hi, Michael.

Thanks for your advice - I'm pulling it now...


It's running, but very slowly, and "mafft" is only running on one core
even though there are 24 cores available and the "mafft" command-line
specifies 12 cores. I think it might be caused by running it on an AMD
Opteron 6000 that does not support SSE2 instructions, but any advice


FYI: Mafft does not appear to use SSE2 in its codebase. I checked and 
the 32-bit mafft 7.467-1 binaries have no SSE2 operands. The 64-bit 
version (amd64) does use SSE2, probably due to optimizations by the 
compiler.


Anyhow, I thought the AMD Opterons are 64bit? Then the do support SSE2 
for sure and 
https://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_6100-series_%22Magny-Cours%22_(45_nm) 
says they support SSE3 as well.


Sorry, my careless slip: I meant SSE4 - I had a problem with "salmon" 
recently running on AMD64 that turned out to be compiled with SSE4. As 
it happens, removing the SSE4 flag did not affect performance, so 
upstream changed it for me  :-)


  https://github.com/COMBINE-lab/salmon/issues/500


about VIP would be welcome - It's been running for a week now :-(


Could be that mafft has reached a point in the computation that is still 
single threaded.


Maybe, but it's taking a very l o n g time :-(

Thanks for your heads-up about the VIP2 container,

  Tony.

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VIP

[Tony Travis]

Re: https://github.com/keylabivdc/VIP

Hi,

Does anyone have experience of running VIP?

I've been trying to get it working under Ubuntu 18.04/20.04 with 
Debian-Med installed in a Bioconda environment, but I've only managed to 
get it running in the author's Ubuntu 14.04 VIP Docker container...


It's running, but very slowly, and "mafft" is only running on one core 
even though there are 24 cores available and the "mafft" command-line 
specifies 12 cores. I think it might be caused by running it on an AMD 
Opteron 6000 that does not support SSE2 instructions, but any advice 
about VIP would be welcome - It's been running for a week now :-(


We're using the pipeline to check Tetse fly microbiota for viruses, but 
it may also be useful for Covid-19 work because the host databases are 
human by default.


Thanks,

  Tony.

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Re: Help from bioinformaticians needed! (Was: Bug#964101: tiddit: generates extremely large file during autopkgtesting)

[Tony Travis]

On 02/07/2020 16:00, Andreas Tille wrote:

Control: tags -1 help

See below.  Please help Nilesh finding a smaller data set.


Hi, Andreas and Nilesh.

Some info here about the data-sets used to benchmark TIDDIT:


https://f1000researchdata.s3.amazonaws.com/supplementary/11168/88aee70a-7a62-48aa-8499-e4e00688348c.pdf


HTH,

  Tony.

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Re: don't copy from there Re: conda

[Tony Travis]

On 24/05/2020 12:33, Rebecca N. Palmer wrote:
Note that we probably can't use code from this package to improve ours: 
I can't find any packaging code in the conda source on GitHub (BSD-3 
licensed), and repo.anaconda.com has legal restrictions, including on 
redistribution:

https://know.anaconda.com/TOS.html


Hi, Rebecca.

I'm not arguing against Debian-Med (re)packaging "conda", just bringing 
to everyone's attention that the Anaconda .deb repo exists. I routinely 
use "Miniconda" to bootstrap Bioconda. I also use with the wrapper that 
I posted here to avoid conflicts with the APT-managed system packages.


The Anaconda .deb installs "conda" in /opt/conda, which is where it 
should go. It does not put things in /usr/local where they are likely to 
be referenced by the system python/python3 etc. causing conflicts. I 
install into /opt/bioconda[23] and put the wrappers in /usr/local/bin.


However, end users of conda are probably planning to use it to install 
packages from there (its default repo), so would be subject to these 
restrictions anyway.  Hence, for such users, this is not a reason to 
avoid _using_ this conda .deb.


Yes, installing from the .deb is a lot more convenient than bootrapping 
"conda" using Minicona. That was the main reason to suggest Debian-Med 
packaging "conda".


Discussion in the conda bug tracker, mentioning both this repo and the 
possibility of adding conda to Debian itself:

https://github.com/conda/conda/issues/1235


I read the discussion there before posting my message to Steffen on the 
list. There are some very ill-informed comments in the discussion. In 
particular, installing packages into /usr/local causes many problems 
because, as I mentioned, the system-managed python* pick up packages in 
/usr/local as well as the system-managed libraries. Using "bioconda" 
with my wrappers avoids the "conda" envs conflicting with the system, 
but allows the envs to see the system-managed packages themselves.


In my experience, it is difficult to avoid people creating per-user 
installations of *conda or R for that matter, in their home directories 
resulting in ridiculous levels of file duplication and ill-configured 
instances leading to different problems for different users. I use a 
root-installed shared instance to avoid that and a wrapper to avoid the 
shared instance conflicting with any of the system-managed packages.


An Anaconda or Debian-Med .deb package is a very effective way to get 
control back into a 'democratised' software environment where users can 
customise their own view without causing problems for anyone else on the 
system, while still maintaining a well-managed core "conda" system.


Bye,

  Tony.

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Re: Infrastructure for next Covid-19 Sprint

[Tony Travis]

On 23/05/2020 20:16, Steffen Möller wrote:

Heya,

I understood that it was a bit difficult with IRC to orchestrate the
participants on the last Sprint.  I am not so much worried about the old
timers (not sure they need a Sprint in the first place) but the
newcomers certainly benefit from something less clumsy and an
integration of sound and vision (https://xkcd.com/1782/). And if we
indeed plan to have some fancier presentation by some upstream devs
then, well, in my very humble opinion IRC is just a no-go.

There is https://discord.com/open-source out there which I started to
like. There are some BOINC and Gridcoin channels via which I got in
contact. Any better ideas on your sides?


Hi, Steffen

Gavin Henry, who contributes to Open Source projects (e.g. OpenLDAP) is 
hosting a public Jitsi-Meet on his SureVOIP company servers in Aberdeen:



https://meet.surevoip.co.uk/


Any interest?

  Tony.

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Re: Please help with Conda packaging [Was: Bug#926416: ITP: conda -- OS-agnostic, system-level binary package manager and ecosystem]

[Tony Travis]

On 23/05/2020 19:56, Steffen Möller wrote:

[...]

Does this make us packaging "conda" for Debian-Med redundant?


I don't know, yet. It likely would if this was a regular Debian
repository that this would be installed from, not from below conda.io.
And I need to look what exactly "rpm-Debian" means. But we can certainly
learn from it.


Hi, Steffen

It looks like a 'normal' Debian repository to me:

root@sei:~# cat /etc/apt/sources.list.d/conda.list 
deb [arch=amd64 signed-by=/usr/share/keyrings/conda-archive-keyring.gpg] https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main



root@sei:~# apt policy conda
conda:
  Installed: 4.8.3-0
  Candidate: 4.8.3-0
  Version table:
 *** 4.8.3-0 500
500 https://repo.anaconda.com/pkgs/misc/debrepo/conda stable/main amd64 
Packages
100 /var/lib/dpkg/status
 4.7.10-0 500
500 https://repo.anaconda.com/pkgs/misc/debrepo/conda stable/main amd64 
Packages
 4.6.14-0 500
500 https://repo.anaconda.com/pkgs/misc/debrepo/conda stable/main amd64 
Packages
 4.5.12-0 500
500 https://repo.anaconda.com/pkgs/misc/debrepo/conda stable/main amd64 
Packages
 4.5.11-0 500
500 https://repo.anaconda.com/pkgs/misc/debrepo/conda stable/main amd64 
Packages


HTH,

  Tony.

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Re: Please help with Conda packaging [Was: Bug#926416: ITP: conda -- OS-agnostic, system-level binary package manager and ecosystem]

[Tony Travis]

On 13/04/2019 06:01, Andreas Tille wrote:

On Fri, Apr 05, 2019 at 02:31:53PM +0200, Andreas Tille wrote:

On Fri, Apr 05, 2019 at 12:00:29PM +0200, Olivier Sallou wrote:

It tries to switch from different environments and fails at default one
which is /usr (no write access)


I think tests calling self.basic_posix should be disabled in
test_activate.py


Done and pushed - feel free to change it yourself in case you want to
make further changes.


Any more hints for the remaining test failures?


Hi, Andreas.

After reading Steffen's message about "conda" on the Wiki, I cloned your 
version from:



https://salsa.debian.org/med-team/conda


In the course of trying to work out how to build and install "conda" I 
came across the "anaconda"RPM and Debian Repositories for Miniconda:



https://conda.io/projects/conda/en/latest/user-guide/install/rpm-debian.html


I added the "anaconda" Debian repository on my computer "sei" and 
installed the "conda" package without any issues under Ubuntu-MATE 18.04 
LTS - It provides an up-to-date "conda":



root@sei:~# source /opt/conda/etc/profile.d/conda.sh
root@sei:~# which -a conda
/opt/conda/condabin/conda
root@sei:~# conda -V
conda 4.8.3


Does this make us packaging "conda" for Debian-Med redundant?

Bye,

  Tony.

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Re: https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/2nd-Covid-19-Hackathon

[Tony Travis]

On 23/05/2020 01:57, Steffen Möller wrote:

Hello,

We had a nice and friendly Debian Med Covid-19 fireside this, well, 
"evening" my time. Quite some of us felt prepared to invest their time 
into a revisited Covid-19 Sprint. On 
https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/2nd-Covid-19-Hackathon 
I put my recollection what we had discussed/thought about. Please give 
it a spin.


Hi, Steffen.

Sorry I been quiet lately, but I am still lurking on the list :-)

I read your musings on the Wiki...

Re: Installing using your "conda" package - I've been struggling a bit 
recently to install the previous QIIME 1.9.1 under bioconda and get a 
strange warning about the CUDA driver, so I'll have a try using your 
"conda" instead and let you know how I get on. I've managed to install 
QIIME 1.9.1 manually, using a combination of "conda" and "pip" under 
"bioconda2", but the Bioconda receipe doesn't work (reports the CUDA 
error). My colleague at the IAEA in Vienna wants to analyse new data 
using QIIME 1.9.1 for comparision with previous analyses. We've been 
using a Bio-Linux 8.0.7 VM, but it will be faster if we can go native!


I think I've told you about my "bioconda" wrapper before, which I use to 
 isolate the bioconda environment from the APT-managed system 
(attached). This avoids the conflicts between "pip/pip3" and APT-managed 
packages.


Bye,

  Tony.

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#!/bin/bash
#@(#)bioconda3.sh  2019-09-20  A.J.Travis

#
# Wrapper for Bioconda Python environment
#

exec /bin/bash --rcfile /usr/local/bin/bioconda2.rc



bioconda2.rc
Description: application/vnd.kde.kxmlguirc
#!/bin/bash
#@(#)bioconda3.sh  2019-02-23  A.J.Travis

#
# Wrapper for Bioconda Python environment
#

exec /bin/bash --rcfile /usr/local/bin/bioconda3.rc



bioconda3.rc
Description: application/vnd.kde.kxmlguirc

Re: Company info

[Tony Travis]

On 01/04/2020 15:55, Ben Tris wrote:

to Tony Travis.

Sorry for causing confusing,

I will contact Jan.


Hi, Ben.

No problem and Andreas encourages our discussions here to be open!

It's a long time since I was working with Jan, but he may remember :-)

Bye,

  Tony.

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Re: Company info

[Tony Travis]

On 01/04/2020 12:45, Ben Tris wrote:

I wonder if you know

Information on Dutch government:

https://lci.rivm.nl/richtlijnen/covid-19

https://www.radboudumc.nl/nieuws/2020/onderzoek-naar-betere-bescherming-zorgmedewerkers-tegen-infectie-coronavirus

leads to:

https://www.modernatx.com/

I wonder if that company is known.

Do you know what free technologies they use.

If not:

Could we ask what  technology they use?

And if that technology is free.

If not, how we can help them to make it free?


Hi, Ben.

This is the English page of RIVM:


https://www.rivm.nl/en


I worked with people from RIVM some years ago on an EU Framework 6 
project called "NuGO" (Nutritional Genomics Organisation) and we used 
"Bio-Linux" to create a distributed bioinformatics infrastructure. As 
you may know, the Debian-Med team have packaged most of what used to be 
in Bio-Linux within the "med-bio" meta-package for Debian/Ubuntu.


My contact at RIVM was Jan van der Lann (in CC) who might be able to 
give more information about what RIVM are doing in relation to Covid-19.


Bye,

  Tony.

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Re: https://github.com/nf-core/covid19 - nextflow pipeline

[Tony Travis]

On 24/03/2020 14:37, Steffen Möller wrote:

[...]

  "please only use Conda as a last resort"

;) You read something else elsewhere.


Hi, Steffen.

No, I read it here:


https://github.com/nf-core/covid19#quick-start
Quick Start

i. Install nextflow

ii. Install either Docker or Singularity for full pipeline reproducibility 
(please only use Conda as a last resort; see docs)


That's why I thought it would be difficult to package things for Debian.

FWIW,

  Tony.

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Re: https://github.com/nf-core/covid19 - nextflow pipeline

[Tony Travis]

On 23/03/2020 14:38, Steffen Möller wrote:

Dear all,

With the enormous difficulties to get bcbio into our distribution (a
considderable list of sequential dependencies for nim, java libraries,
golang-bio, sigh) I also had an eye on nf-core and their
nextflow-based workflows. I think I uploaded the one or other package
from their dependencies but, well, treated it more like an inspiration
than a project. From what I oversee it is far easier to address than bcbio.
[...]


Hi, Steffen.

I've just had a look at the "nf-core" repo and read this:

  "please only use Conda as a last resort"

They recommend running "nf-core" under Docker or Singularity, which I 
believe would make it unsuitable for packaging as part of "med-bio".


I'm currently running "bcbio_nextgen" under Ubuntu-MATE 18.04 + med-bio, 
but the developers advised me NOT to use the 'external' versions of 
tools like "bwa" or "bowtie2" from Debian-Med but install everything 
isolated from the 'system'.


I think this sort of application is more effort than it's worth to 
package for "med-bio". However, I think that a bare-bones package 
equivalent to bootstrapping "bioconda" using "miniconda" would be 
worthwhile to provide a ready-to-use "bioconda" within Debian-Med.


Bye,

  Tony.

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med-bio under Ubuntu 20.04

[Tony Travis]

Hi,

I've now upgraded two systems from Ubuntu 18.04 to 20.04rc without any 
issues concerning packages and dependencies in med-bio or med-bio-dev.


Thanks for all the hard work done by the Debian-Med team to make this 
bioinformatics software easy to install and use even under Ubuntu :-)


  Tony.

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Re: BUG in ncbi-blast+

[Tony Travis]

On 17/01/2020 11:57, Andreas Tille wrote:

[...]
Can you please add some kind of example code that enables us to
reproduce the issue?  We could add it to the autopkgtest

   
https://salsa.debian.org/med-team/ncbi-blastplus/blob/master/debian/tests/run-unit-test

to verify that this issue is solved.


Hi, Andreas.

I'm not sure how this can be tested without tracing attempts by "blastn" 
to stat and read /etc/ncbi/.ncbirc, as I showed in my previous email.


The BUG appears to be caused when the NCBI environment variable is 
undefined. Setting NCBI to the installed location of the default config 
file under Ubuntu fixes the problem:



ajt@beluga:~$ export NCBI=/etc/ncbi
ajt@beluga:~$ strace blastn |& fgrep .ncbirc
stat("./.ncbirc", 0x7ffc01d0e2c0)   = -1 ENOENT (No such file or directory)
stat("/home/ajt/.ncbirc", 0x7ffc01d0e2c0) = -1 ENOENT (No such file or 
directory)
stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
lstat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
openat(AT_FDCWD, "/etc/ncbi/.ncbirc", O_RDONLY) = 3
stat("./.ncbirc", 0x7ffc01d0eae0)   = -1 ENOENT (No such file or directory)
stat("/home/ajt/.ncbirc", 0x7ffc01d0eae0) = -1 ENOENT (No such file or 
directory)
stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0


This behaviour is consistent to what NCBI describe:


https://www.ncbi.nlm.nih.gov/books/NBK279695/


A unit test would need to know where the deb stores ".ncbirc" and strace 
the execution of "blastn" to make sure the executable finds the default 
config file. If NCBI is unset, it looks for "/etc/.ncbirc". However, the 
default location it is installed to under Ubuntu is "/etc/ncbi/.ncbirc".


HTH,

  Tony.

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Re: BUG in ncbi-blast+

[Tony Travis]

On 17/01/2020 09:10, Andreas Tille wrote:

[...]

Please let me know the proper way to report this BUG in med-bio?


Nitpicking: You do not iwant to report to med-bio (which is a different
package) - you want to report to the Debian BTS.  Since I know you are
usually using Ubuntu please refer to


Hi, Andreas.

OK, and thanks for explaining: I thought that because "ncbi-blast+" is a 
dependency of the "med-bio" metapackage I should report the BUG here...



[...]
since a mail needs to be sent by reportbug and you need a valid
smtphost (in case you do not have any valid one configured on your
local machine).

Hope this helps and thanks for reporting issues to Debian


Yes, it helps a lot :-)

I tried "reportbug", but Ubuntu prefers to use "ubuntu-bug" and a 
web-form on 'Launchpad' instead so I've reported the BUG there:



https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/1860109


I guess this will eventually find its way to the Debian BUG tracker.

Thanks for your help,

  Tony.

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BUG in ncbi-blast+

[Tony Travis]

Hi,

While attempting to use NCBI "blastn" from behind a proxy, I traced the 
execution of "blastn" to check if it was reading the default 
"/etc/ncbi/.ncbirc" file where I put my proxy config in because it 
wasn't working.


In fact, this file is never stat'ed or read:


ajt@beluga:~$ strace blastn |& fgrep .ncbirc
stat("./.ncbirc", 0x7fff8bbc0200)   = -1 ENOENT (No such file or directory)
stat("/home/ajt/.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or 
directory)
stat("/etc/.ncbirc", 0x7fff8bbc0200)= -1 ENOENT (No such file or directory)
stat("/usr/bin/.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or directory)


My "~/.ncbirc" file is read correctly, so I'm using that instead.

Please let me know the proper way to report this BUG in med-bio?

Thanks,

  Tony.

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Re: Debian Med Sprint 2020 in Berlin?

[Tony Travis]

On 03/12/2019 09:37, Sascha Steinbiss wrote:

Hi all,


If we agree to have the sprint in Berlin and also agreed on a date, I would be 
happy to set up a wiki page.


Wiki page is open!

->
https://wiki.debian.org/Sprints/2020/Debian%20Med%20Sprint%20Feb%202020%2C%20Berlin


Hi, Sascha.

Sorry, I can't attend the next Sprint in Berlin on Feb 8/9 in 2020 
because of prior commitments. However, I really appreciate the great 
work that the Debian-Med team are doing!


I continue to promote Bio-Linux 9 as Ubuntu-MATE 18.04 LTS + med.bio

Thanks,

 Tony.

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Re: Refs to Conda - gone through the med/bio task list

[Tony Travis]

On 18/10/2019 13:06, Steffen Möller wrote:

[...]
In summary, I think the effort should be continued. I feel personally 
somewhat responsible for the packages in our bio-* task lists. Beyond 
that, we either convince our community that the effort is worth it - or 
likely it is not worth it. Without examples how this all can be brought 
to some good use, we should possibly invest our energy elsewhere.


Hi, Steffen.

I install a shared copy of "bioconda" in /opt and use a wrapper to avoid 
conflicts between OS versions of the Python scripts and libraries and 
any versions that are dependencies of particular "conda" environments:



#!/bin/bash
#@(#)bioconda3.sh  2019-02-23  A.J.Travis

#
# Wrapper for Bioconda Python environment
#

exec /bin/bash --rcfile /usr/local/bin/bioconda3.rc



#!/bin/bash
#@(#)bioconda3.rc  2019-10-09  A.J.Travis

#
# Wrapper for Bioconda Python environment
#

eval "$(/opt/bioconda3/bin/conda shell.bash hook)"


[And a similar wrapper for "bioconda2"]

One reason for using "bioconda" is that it makes it practical to have 
multiple versions of applications installed, which is often important 
(e.g. to complete a project using the same version of an application, 
while upgrading the system to use the latest version for new projects.


However, it's a recipe for disaster to follow the default "miniconda" 
bootstrap instructions that modify ".bashrc" (or the profile of the 
shell you are using) and duplicate the entire "bioconda" installation 
for each user in their own login directory.


Using a shared installation is better, but needs to be done using a 
wrapper to avoid breaking the OS environment for "root" and similarly 
the 'normal' login environment for other users, who can still add their 
own environments without needlessly duplicating the core applications.


I also note that "conda" can cooperate with "pip" and "pypi" to avoid 
conflicts. I think it would be useful for "conda" to be aware of any 
conflicting packages managed by "apt" in a similar way. The same problem 
also occurs when managing packages directly using R, which conflict with 
packages managed by "apt", but this can be mitigated to some extent by 
managing R in isolated "conda" environments instead of "apt" packages.


HTH,

  Tony.

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Re: PIQUE packaging (Was: request for r-cran packages)

[Tony Travis]

On 02/07/2019 15:08, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 04:15:11PM +0100, Tony Travis wrote:

2. Is there any description of PIQUE that could be used as long
   description for the package.  I've checked doc/pique_manual.odt
   but despite its filename it says it is the ParSNP manual
   (btw, parsnp is packaged) and doc/pique_tutorial.odt does
   also not contain anything that would enlighten me about PIQUE
   at first sight.
   Feel free to simply replace the FIXME in
https://salsa.debian.org/med-team/pique/blob/master/debian/control


Yes, I'll sort that out: We called it "ParSNP" at first, but I subsequently
discovered that someone has already used that name!


I've stumbled upon old mails.  Emmax is in new queue since some time but
final PIQUE packaging is just blocked due to missing long description.


Hi, Andreas.

OK, I'll sort that out.

Thanks for the work you've done packaging "PIQUE",

  Tony.

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Re: FW: New contact form received

[Tony Travis]

On 01/07/2019 16:28, david hancock wrote:

H[...]
We're trying to figure out how hard it would be to put an RPM somewhere 
public and permanent that would server as something that could be cited 
now, and in the future.


Hi, Dave.

That would be 'deb' package for Debian-Med, or an 'rpm' for RHEL/CentOS.

HTH,

  Tony.

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Re: FW: New contact form received

[Tony Travis]

On 01/07/2019 15:45, Andreas Tille wrote:

[...]
To be a bit picky about wording: The Debian Med team has packaged lots
of the software for main Debian that used to be provided by Bio-Linux.
While I remember that Bio-Linux members like Tim Booth contributed code
to Debian Med I do not remember that I was able to drain a source
package from Bio-Linux and "port" this into a Debian package since it
seems there were no such source packages available that would rectify
the word "porting".


Hi, Andreas.

OK, I accept your correction because the original NEBC Bio-Linux deb's 
were hand-crafted binary deb packages created by Tim and Bela from their 
'tarball' installations of software into /usr/local, which caused a 
litany of problems for Bio-Linux, but I had no part in that decision!



[...]
Tony, I've added an entry to the "missing in Bio-Linux" list[1] (thanks
to Carnë Draug for the pointer to the webarchive).  If there is any
software requested by Bio-Linux users pretty please maintain this list.
Random mails to our mailing list are not at all a safe way to get
anything packaged.  The technical way to ask for packaging is filing an
"RFP" bug report - but we agreed upon the list[1] to lower the barrier.


Sorry, I've done it the wrong way again...


However, I wonder how much promising it will be to ask for software
which has no maintained web page any more, the web archive change is
from 2007 and there is no visible source code.  I'd support anybody
who wants to give the packaging of it a try but I'll spend my time
rather on more promising code.


I believe Dave has the source code (he is the author of maxdView).

Thanks,

  Tony.

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Re: FW: New contact form received

[Tony Travis]

On 01/07/2019 14:07, Timms-Wilson, Tracey wrote:




-Original Message-
From: David Hancoc [mailto:m...@davidhancock.com]
Sent: 01 July 2019 14:07
To: Timms-Wilson, Tracey ; Timms-Wilson, Tracey

Subject: New contact form received

You have received a new contact form message.
Name : David Hancock
Email : m...@davidhancock.com
Message : Hello,

Some researchers have been in touch with me. They are trying to cite
maxdView - software that we used to host.

They still use vintage versions of it, but are wondering how to cite it  
properlty.
Specifically so that other people can use it.

The download packge is still bundled into BioLinux, but the stand-alone
download pages, previously hosted by  CEH,  have disappeared.

Any chance that this can be re-instated?


Hi, David.

Tracey forwarded your email to me because I'm last-man-standing on the 
Bio-Linux project, which is now effectively abandoned by NERC/EOS and 
Bio-Linux 8 is no longer supported either by NERC/EOS, or by me...


During the Bio-Linux project, we collaborated a lot with the Debian-Med 
team, who ported many of the most useful packages from Bio-Linux to 
Debian-Med. Indeed, our strategy has been to avoid using the 'orphaned' 
NERC repositories that we no longer have access to update or modify.


I attended the 2019 Debian-Med Sprint in Vilnius earlier this year and 
presented my ideas about continuing development of Bio-Linux 9 within 
the Debian-Med project. The Debian-Med team have been very supportive:



https://wiki.debian.org/Sprints/2019/DebianMed2019



I've CC'ed your email to the Bio-Linux and Debian-Med mailing lists in 
case anyone is willing to volunteer to update the existing Bio-Linux 8 
"maxdView" package and make it available for Debian/Ubuntu in "med-bio".


Please post a message about the development and future of "maxdView".

Thanks,

  Tony.

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bio-linux-desktop

[Tony Travis]

Hi, Andreas.

Sorry about my slow progress on this project...

I've been creating "bio-linux-desktop" .iso's manually from the 'task' 
you created and even though not all of the packages were installed the 
resulting .iso is already > 6GB, which is too big to write to a DVD.


I'll continue doing this manually for now until I come up with a sub-set 
of "med-bio" that is similar to Bio-Linux 8 and will fit in a 4GiB .iso.


Bye,

  Tony.

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Re: FW: Bio linux download

[Tony Travis]

On 24/04/2019 20:29, Dylan Aïssi wrote:

Hi Graham,

Le mer. 24 avr. 2019 à 21:19, Graham Inggs  a écrit :


Is this LP: #1777165 [1]?  Let's get this fixed, I'm happy to sponsor
a SRU [2] upload.



I am preparing the fix [1], I will ping you when it is ready.

Best,
Dylan

[1] https://salsa.debian.org/med-team/metaphlan2/commits/ubuntu/bionic


Hi, Dylan.

I've installed the "metaphlan2" package from Ubuntu "bionic-proposed" 
successfully, with no errors reported. If "metaphlan2" is installed, 
"med-bio" will install without errors in Ubuntu-MATE 18.04.2 LTS:



ajt@beluga:~$ apt policy metaphlan2
metaphlan2:
  Installed: 2.7.5-1ubuntu1
  Candidate: 2.7.5-1ubuntu1
  Version table:
 *** 2.7.5-1ubuntu1 400
400 http://gb.archive.ubuntu.com/ubuntu bionic-proposed/universe amd64 
Packages
400 http://gb.archive.ubuntu.com/ubuntu bionic-proposed/universe i386 
Packages
100 /var/lib/dpkg/status
 2.7.5-1 500
500 http://gb.archive.ubuntu.com/ubuntu bionic/universe amd64 Packages
500 http://gb.archive.ubuntu.com/ubuntu bionic/universe i386 Packages


Please let me know if/when the broken version of "metaphlan2" will be 
updated in the Ubuntu repositories?


Thanks,

  Tony.

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Re: FW: Bio linux download

[Tony Travis]

On 25/04/2019 19:11, Graham Inggs wrote:

On Wed, 24 Apr 2019 at 23:42, Tony Travis
 wrote:

I reported the bug and provided a patch - What else should I have done?


Subscribing the 'ubuntu-sponsors' team to the bug would have made it
visible to someone who could have done the upload for you.

It's mostly only the packages supported by Canonical that have subscribers.

There's also a bot that finds patches, but it seems it only finds
attachments, not inline patches.


Hi, Graham.

OK, will do that next time :-)

Thanks,

  Tony.

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Re: FW: Bio linux download

[Tony Travis]

On 24/04/2019 21:20, Graham Inggs wrote:

Hi

On Wed, 24 Apr 2019 at 21:30, Dylan Aïssi  wrote:

I am preparing the fix [1], I will ping you when it is ready.


Uploaded, thanks!

For future reference, the general procedure to get a fix into Ubuntu
is to attach a patch and subscribe 'ubuntu-sponsors' to the bug.


Hi, Graham and Dylan.

I reported the bug and provided a patch - What else should I have done?

Bye,

  Tony.

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Re: FW: Bio linux download

[Tony Travis]

On 24/04/2019 14:55, Timms-Wilson, Tracey wrote:

*From:*Shaun Allingham [mailto:s.alling...@derby.ac.uk]
*Sent:* 24 April 2019 14:37
*To:* Timms-Wilson, Tracey 
*Subject:* Bio linux download

Hi, I am trying to download Biolinux on a USB stick but once i have 
finished the initial download the only option i get is to burn it onto a 
CD. Is there something i am missing?


Hi, Shaun.

Tracey forwarded your message to me and I've CC'ed my reply to the 
Bio-Linux mailing list in case anyone else has the same problem.


We've done a 'point' release of Bio-Linux 8.0.8 that you can download:


http://environmentalomics.org/bio-linux-8-0-8-2/


Please read the NERC/EOS documentation about how to create a USB-stick:


http://environmentalomics.org/bio-linux-installation/


Please note that Bio-Linux 8.0.7/8 are both based on Ubuntu 14.04 LTS, 
which will reach it's end of life this month (April 2019) so I do not 
recommend using Bio-Linux 8, which is no longer supported by NERC/EOS.


I recommend downloading Ubuntu-MATE 18.04 LTS and creating a bootable 
USB-stick from that, and use the USB-stick to install Ubuntu-MATE 18.04 
permanently onto a hard disk (or an external USB disk):



https://ubuntu-mate.org/download/


Then, boot from the hard disk and install "med-bio" and "med-bio-dev" 
from the Debian-Med project onto the Ubuntu-MATE 18.04 instance:


  sudo -i
  apt update
  apt install med-bio med-bio-dev

[Note: There is a problem installing "metaphlan2" under Ubuntu 18.04]

Most of the packages in Bio-Linux 8 are now available in the Ubuntu 
repository thanks to the work of the Debian-Med team. Please post a 
message to the Debian-Med mailing list if you decide to try med-bio out.


I can provide you with a pre-release Bio-Linux 9-alpha 'live' USB-stick 
based on Ubuntu-MATE 18.04 + packages from "med-bio" if you send me a 
stamped addressed padded envelope to the address in my signature below.


HTH,

  Tony.

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Re: Please help with Conda packaging [Was: Bug#926416: ITP: conda -- OS-agnostic, system-level binary package manager and ecosystem]

[Tony Travis]

On 04/04/2019 21:30, Andreas Tille wrote:

Hi,

I'd like to ask for help with packaging Conda.  I think its good to have
it packaged since several users use it and finally we want to support
our users as best as possble.  I have commited an initial packaging to

   https://salsa.debian.org/med-team/conda

To build and install you need python-pycosat which is in new queue
currently.  You can clone and build it for your local tests from

   https://salsa.debian.org/med-team/python-pycosat

The Conda build has 5 remaining failures which I do not understand.  I
wonder if some volunteer is sure that these failures either can be
ignored since it makes no sense to run this test in a pbuilder chroot or
possibly fix the test to make it pass.


Hi, Andreas.

I want to volunteer to help, but I don't know how to use pbuild 
properly! I'll give it a try and let you know how I get on ;-)


Bye,

  Tony.

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Re: UTAP

[Tony Travis]

On 31/03/2019 12:51, Marilyn Safran wrote:

Hi Tony,

Feel free to try out the software without using a docker container,
and prepare and distribute the Debian-Med package.

Please let us know when that package becomes available, and how to
access it.

And please make sure to acknowledge our paper so that others can
contact us if needed.


Hi, Marilyn.

The first step is for me to let the Debian-Med team know about UTAP, by 
CC to the Debian-Med mailing list, and for me to try it without using a 
Docker container to see what other software dependencies UTAP requires.


@debian-med list,

I'm interested in packaging UTAP:


https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2728-2


UTAP: User-friendly Transcriptome Analysis Pipeline

RNA-Seq technology is routinely used to characterize the transcriptome, 
and to detect gene expression differences among cell types, genotypes 
and conditions. Advances in short-read sequencing instruments such as 
Illumina Next-Seq have yielded easy-to-operate machines, with high 
throughput, at a lower price per base. However, processing this data 
requires bioinformatics expertise to tailor and execute specific 
solutions for each type of library preparation. In order to enable fast 
and user-friendly data analysis, we developed an intuitive and scalable 
transcriptome pipeline that executes the full process, starting from 
cDNA sequences derived by RNA-Seq [Nat Rev Genet 10:57-63, 2009] and 
bulk MARS-Seq [Science 343:776-779, 2014] and ending with sets of 
differentially expressed genes. Output files are placed in structured 
folders, and results summaries are provided in rich and comprehensive 
reports, containing dozens of plots, tables and links. Our User-friendly 
Transcriptome Analysis Pipeline (UTAP) is an open source, web-based 
intuitive platform available to the biomedical research community, 
enabling researchers to efficiently and accurately analyse transcriptome 
sequence data.


The software is available under GPLv3:


https://utap.readthedocs.io/en/latest/
I've contacted the upstream authors Refael Kohen, Dena Leshkowitz, and 
Marilyn Safran who are willing to let us package and distribute their 
UTAP software for Debian-Med.


Thanks,

  Tony.

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Bio-Linux 8 EOL

[Tony Travis]

Hi,

Bio-Linux 8 will reach its EOL (End Of Life) in April 2019 when Ubuntu 
14.04 LTS reaches its EOL and Bio-Linux 8 will no longer be supported.


Bio-Linux 9 is still a work in progress, but I recommend replacing any 
Bio-Linux 8 instances with a clean install of Ubuntu-MATE 18.04 LTS:



https://ubuntu-mate.org/download/


Please do NOT attempt to upgrade Bio-Linux 8 because many packages will 
be broken and the upgrade process will be error-prone. After installing 
Ubuntu-MATE 18.04 LTS, install the Debian-Med and x2go packages:


  sudo -i
  apt update
  apt install med-bio med-bio-dev
  apt install x2goserver

Also install these security packages:

  apt install fail2ban
  apt install rkhunter
  apt install chkrootkit

In due course, I will announce the Debian-Med "bio-linux" meta-packages:

  bio-linux-desktop
  bio-linux server

Please post messages about any problems with this upgrade and ideas 
about future development of Bio-Linux to the Debian-Med mailing list.


Thanks,

  Tony.

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Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 21:53, Andreas Tille wrote:

[...]
You are welcome.  Emmax is now also uploaded.  Please cross fingers
that ftpmaster is convinced by the d/copyright wording.


Hi, Andreas.

My Indian colleague has encountered run-time errors in PIQUE due to a 
missing Slurp.pm module - PIQUE has a dependency on:


  libfile-slurp-perl

[This was already present in my system, but not in his]

Bye,

  Tony.

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Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 17:01, Andreas Tille wrote:

[...]
Well, I *personally* think that your decision to rely on those PPA and
hardly upgradable releases is asking for trouble at some point in time.
You are refusing the help of the men power of the Debian Med team who is
usually as quick as backports ftpmaster response to provide needed
backports.  But that's your decision and should not be discussed here.


Hi, Andreas.

I'm not refusing anyone's help!

This is not a problem with Debian, it's really a problem with Ubuntu's 
relationship to Debian - Please feel free to tell me I would not have 
these problems if I used Debian :-)


I only want to use Ubuntu LTS releases which, I now know, means I won't 
get all the up-to-date things you are contributing to Debian because LTS 
are not rolling releases. So, I'm making the same pragmatic choice that 
Tim Booth made in Bio-Linux 8 to use Michael Rutter's Ubuntu PPA's. I 
wish Ubuntu 18.04 had the up-to-date Debian packages, but it does not.



Sorry again about the false alarm asking Debian-Med to package the three R
libraries that I needed. They are fully supported in the CRAN 3.5 PPA.

Hope this doesn't put you off packaging PIQUE!


It seems I did not made my point clear enough.  PIQUE is depending from
those R packages and thus theses need to be packaged before PIQUE.
Luckily this is done and the packages are just waiting for ftpmaster.
The same is true for EMMAX (I mean the same way this is needed - thanks
to https://lists.debian.org/debian-med/2019/03/msg00085.html we hopefully
can make ftpmaster accepting it).

Please confirm that you understood that a package can only exist in
Debian if all its preconditions are packaged.


I do understand, and thank you for uploading the three r-cran packages.

Bye,

  Tony.

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Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:36, Andreas Tille wrote:

On Wed, Mar 20, 2019 at 04:06:33PM +0100, Steffen Möller wrote:

I can package one or two of these R packages. Please direct me which one
I should address first.


None, all are in new as I wrote here

https://lists.debian.org/debian-med/2019/03/msg00075.html

I'd **strongly** recommend to everybody who wants to package GNU R
packages to read and understand this mail to save **a HUGE amount of
time** and by doing so also deliver policy conform and up to date
packaging.


Hi, Andreas.

I apologise for my ignorance but, in fairness to me, it was not clear 
why the Ubuntu 18.04 r-cran packages are so out of date and I did not 
fully appreciate the discussions that had gone on about deprecating R 
version 3.4 in Ubuntu 18.04 LTS. I know now, and I have taken action.


Thanks for your advice,

  Tony.

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Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:32, Andreas Tille wrote:

On Wed, Mar 20, 2019 at 04:23:44PM +0100, Tony Travis wrote:

Probably trying to do too many things at once just now :-|

Please don't spend any time packaging the R libraries I requested, because
I'm going to use R 3.5 from now on.

Sorry about the false alarm, requesting packaging.


Wait a moment:  pique just needs some R packages, right?  A Debian
package of a GNU R package always builds against the latest packaged
version of R which is currently 3.5.3.  The three packages I uploaded to
new are built against this.  The packaging process itself does not
depend on the R version (funnily enough the only person who thinks so
is the R maintainer but he is de facto wrong in nearly all practical
cases and there were some flames about this ;-) ).

So I guess it was correct that I uploaded the three R packages, right?


Hi, Andreas.

The problem lies with the Ubuntu 'Universe' repository, where all the R 
dependencies are for R version 3.4, even in Ubuntu 18.04 LTS (bionic).


These, as with the out-of-date "Abyss" package in Ubuntu 18.04 all seem 
to be consequences of the same "no rolling release" policy of Ubuntu and 
do not reflect in any way a criticism of Debian. I've got backports 
enabled, but it makes no difference. As Steffen said, in an ideal world 
we would not need to use the PPA's, but as a practical way forward we 
need to because Ubuntu 18.04 is not going to sync with the latest Debian 
packages that, as you said, _are_ using R 3.5.


CRAN is quite clear that R 3.5 is the supported version in Ubuntu bionic 
and, I admit, I didn't know that until I checked today when one of my 
colleagues in India was having problems installing PIQUE under Ubuntu 
18.04 and I started to investigate. In general, I go with whatever is in 
the Ubuntu repositories but, in this case, the repositories are out of 
date with CRAN and I need to use Michael Rutter's PPA's.


Sorry again about the false alarm asking Debian-Med to package the three 
R libraries that I needed. They are fully supported in the CRAN 3.5 PPA.


Hope this doesn't put you off packaging PIQUE!

Bye,

  Tony.

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Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:19, Tony Travis wrote:

On 20/03/2019 16:06, Steffen Möller wrote:


On 20.03.19 13:48, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:
Yes, that would be great if you're willing, but I would struggle to 
do it on

my own despite you explaining to me several times what to do...

Its a pleasure for me to look at this once you fixed

    https://github.com/tony-travis/PIQUE/issues/3

;-)



Hey, congrats, there is version 1.0!

I can package one or two of these R packages. Please direct me which one
I should address first.


Hi, Steffen.

I've decided to move to R 3.5 instead, because Michael Rutter's PPA has 
the packages available for R 3.5 in Zenial [...]


Hi, Steffen.

Er, I meant "bionic" - Don't know where "Zenial" came from!

Probably trying to do too many things at once just now :-|

Please don't spend any time packaging the R libraries I requested, 
because I'm going to use R 3.5 from now on.


Sorry about the false alarm, requesting packaging.

Bye,

  Tony.

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Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:06, Steffen Möller wrote:


On 20.03.19 13:48, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:
Yes, that would be great if you're willing, but I would struggle to 
do it on

my own despite you explaining to me several times what to do...

Its a pleasure for me to look at this once you fixed

    https://github.com/tony-travis/PIQUE/issues/3

;-)



Hey, congrats, there is version 1.0!

I can package one or two of these R packages. Please direct me which one
I should address first.


Hi, Steffen.

I've decided to move to R 3.5 instead, because Michael Rutter's PPA has 
the packages available for R 3.5 in Zenial and the 3.4 versions are now 
deprecated starting from Ubuntu 18.04 LTS. I've just tested installing 
PIQUE under Ubuntu-MATE 18.04 LTS with both of Michael's R 3.5 PPA's.


Sorry about the false alarm re: Packaging the R 3.4 libraries...

However, it's great to have PIQUE packaged!

Bye,

  Tony.

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