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drj11 /
Last active Nov 21, 2019
comments on google-pol-collector

media_saver is empty.

The command line args

The command line args are weird. Perhaps do something like:

main --data uk --ads uk --data all

annoying because it makes me repeat uk, and is slightly non-standard

drj11 /
Last active May 10, 2018
Notes on Refinery

many files in S3 buckets. EG beta-gtc-media

AWS deployment instructions should say something about terraform (they do, sort of).

STACK_NAME constraint isn't correct. Hyphens seems to be allowed.

from shannan, talk to ilya about new directory scheme for S3 uploads (on 1.6.4 ?)

RNAseq for salmon pseudo-alignment, what's stopping the tool working? either tool wrappers need updating to point to GTF, or, tool launching needs to be able to describe the additional GTF parameter.

drj11 / log.txt
Created Mar 6, 2018
Log file for bcbio upgrade
View log.txt
INFO: <cloudbio.flavor.Flavor instance at 0x2b4165870d40>
INFO: This is a ngs_pipeline_minimal flavor
INFO: Reading default fabricrc.txt
DBG []: Using config file /home/md1xdrj/job/out/tmpbcbio-install/cloudbiolinux/cloudbio/../config/fabricrc.txt
INFO: Distribution __auto__
INFO: Get local environment
INFO: CentOS setup
DBG []: NixPkgs: Ignored
INFO: Now, testing connection to host...
INFO: Connection to host appears to work!
drj11 /
Created Mar 2, 2018
Keith Burnett e-mail 2018-03-02

Dear colleagues,

Further to my message yesterday, I want to update you on the work I have been doing nationally in relation to the USS dispute, ahead of what I hope will be a significant meeting between UUK and UCU next week with ACAS.

I have already made public the views this University has conveyed to UUK with regard to talks without preconditions and on seeking agreement around the valuation. Further to this, I have been in touch with other colleagues across the UK as well as the Employers Pension Forum. I am expecting feedback from these discussions on Monday, and I will then meet with colleagues from UCU here in Sheffield on Tuesday so I can share with them what I have learned and listen to their views on this and other matters. I have asked my office to set up this meeting today.

Once again, I am committed to seeking a resolution to this dispute which provides a good, sustainable pension for staff in the interests of both our students and will do all I can to secure a positive conclusion to the curre

drj11 /
Created Mar 2, 2018
Keith Burnett e-amil 2018-03-01

Dear colleagues,

I wanted to write to you in relation to the industrial action which has taken place over the last two weeks in relation to the USS Pensions.

First of all, I want to clarify our local position with regard to industrial action. Concerns have been raised with me that this University will take a particularly punitive approach towards colleagues engaged in action taken short of a strike. While the University reserves the right to make proportionate deductions for partial performance where this is in breach of a contract, I have instructed staff that this will not be applied in the case of rescheduling of lectures missed on strike days. We will carefully look at the advice we provide to staff to reflect this, correcting any impression that this is not the case.

My view on the wider dispute remains one of concern. I am pleased UUK and UCU met for talks this week, and that they have agreed to meet again with ACAS. I hope this meeting will take place early next week. As I have said previously, thes

drj11 /
Created Feb 21, 2018
Keith Burnett e-mail 2018-02-21

Dear colleagues,

Many staff have expressed to me their deep concern about strike action planned for tomorrow regarding the proposed changes to the USS pension scheme, and their desire to avoid a protracted dispute. The University is also keen to avoid a dispute if at all possible and I and other colleagues have spoken to UUK directly in an effort to seek a solution.

The position of our University and Council is that we understand change is necessary to ensure pensions remain sustainable and affordable. Having said that, the University has always sought to ensure any changes extend only to what is necessary to achieve this aim.

There has been much comment on this issue in the media and I recognise there are concerns regarding the valuation underpinning the current proposals for change. We have been in contact with UUK again today to seek clarity over the specific points being raised and are awaiting a response.

It is important that we all have confidence in the valuation process and we are keen to check th

drj11 /
Created Feb 16, 2018
Keith Burnett e-mail 2018-02-16

Dear colleague,

I would like to start this message by thanking all of those who have written to me following the news of my retirement. It has been very humbling to hear from my colleagues and it has certainly made me reflect again on what our University stands for and how this has driven me over the years in Sheffield.

Many of you will have heard me talk about the historic poster displayed in Sheffield's factories which made the case for the establishment of a university which would be 'for the people'. I have found this the most moving of documents because, in it, I have seen the hopes and efforts of those who came before us.

One of the people I particularly relate to is the young Welsh scientist and the Principal of Firth College, John Viriamu Jones, who later went on to found Cardiff University. Like me, he studied physics at Oxford. But Sheffield was where it began and where he made a passionate case for a broad and excellent education that made a difference to the lives of people in this industrial c

drj11 /
Created Jan 31, 2018
isa-api experience

Creating a validator tool, as per the example.

unclear if I should use zip or i_* file. Turns out to be i_* file.

but then, there are warnings relating to finding extra files in the archive. Which can surely only apply to a zip?

We might want to use OrderedDict a bit more (or wait for Python 3.6)?

View gist:8d93ed81935f4899c43d73eeb8bb40b2
On Tuesday 2018-01-23 shortly before 16:24 and after emerging from the south tunnel of the Moore Street roundabout (that is adjacent to the Moore Street Electricity Substation) I espied a motor vehicle that I considered inconsiderately parked, and parked in a manner likely to endanger the public.
The vehicle was parked on the north side of Clarence Lane, close to the tunnel, and more or less opposite the pedestrian entrance to the adjacent car park.
That vehicle was a South Yorkshire Police Mobile CCTV van, registration number YN04 SNY.
Suspecting the vehicle was under the command of the police personnel I had just walked passed in the tunnel,
I returned to the tunnel and attempted to open a conversation with a person who later identified themself as
Paul Cundy, collar number 3088.
I raised my concern that the vehicle was inconsiderately parked.
drj11 /
Created Jan 10, 2018
Keith Burnett emails re retirement

Dear colleagues,

Following the announcement that I will be retiring around my 65th birthday, I have been asked to write a few words to add to those from the Chair of our Council. He is a man whose commitment to the University and its city is unbounded and I am most grateful for his generous words in the announcement he circulated on Monday.

As you might expect, I have been thinking about my retirement for some time. It will be a wrench to leave Sheffield, but I know I'm leaving our University in good shape, with great senior leadership and talent, and dedication to scholarship and teaching at all levels. I am under no illusion that we are perfect, but I have been strengthened to know that I represent such a strong international community of staff and students who share a belief in the difference education can and does make.

Looking back, I am truly grateful that this University chose me to be its Vice-Chancellor more than a decade ago. People told me then that it would be unlike anything else I had experie

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