drj11

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

drj11

arrives with no battery charge instead of partially charged

case frame feels flimsy
camera good (though app makes flipping between front and back camera a bit awkward)
button for taking pictures is okay

but the absolute killer is that it spontaneously reboots.
When I use Google Maps. Like a couple of times an hour.
And also Pokemon Go.

drj11

Installing pywikibot

I recommend you use conda and create a conda env.

On sharc/iceberg

module load apps/python/conda

. activate my_conda_env

drj11

Lots of SNPs from 1 chromosome:

curl 'http://biotech.bmi.ac.cn/3dsnp/api.do?chrom=chr1&position=1000000-2000000&format=json&type=basic'

Probably a good idea to save that in a file while you are messing around.

With that saved in file j:

pretty print the result

drj11

2017-04-24 09:22:56 ERROR    data_set_manager.tasks:513 parse_isatab() - None
2017-04-24 09:47:36 INFO     data_set_manager.isa_tab_parser:1110 get_dataset_name() - Supplied path "/data/media/file_store/temp/johnDD_archive.zip" is not a directory. Assuming ISArchive file.
2017-04-24 09:47:39 INFO     data_set_manager.isa_tab_parser:1139 get_dataset_name() - ISArchive extracted to "/tmp/tmp2sJZho".
2017-04-24 09:47:39 INFO     data_set_manager.isa_tab_parser:1156 get_dataset_name() - Investigation file path: /tmp/tmp2sJZho/i_Investigation.txt
2017-04-24 09:47:39 INFO     data_set_manager.isa_tab_parser:945 run() - Supplied path "/data/media/file_store/temp/johnDD_archive.zip" is not a directory. Assuming ISArchive file.
2017-04-24 09:47:43 INFO     data_set_manager.isa_tab_parser:974 run() - ISArchive extracted to "/tmp/tmpPiu5UD".
2017-04-24 09:47:43 INFO     data_set_manager.isa_tab_parser:703 _create_investigation_file_section_model() - Column 1 in section ONTOLOGY SOURCE REFERENCE has no non-empty cells an

drj11

2017-04-24 08:50:10 INFO     data_set_manager.isa_tab_parser:1110 get_dataset_name() - Supplied path "/data/media/file_store/temp/test_johnDD.zip" is not a directory. Assuming ISArchive file.
2017-04-24 08:50:10 INFO     data_set_manager.isa_tab_parser:1139 get_dataset_name() - ISArchive extracted to "/tmp/tmpmrZshL/test_johnDD/".
2017-04-24 08:50:10 INFO     data_set_manager.isa_tab_parser:1156 get_dataset_name() - Investigation file path: /tmp/tmpmrZshL/test_johnDD/i_11111.txt
2017-04-24 08:50:10 INFO     data_set_manager.isa_tab_parser:945 run() - Supplied path "/data/media/file_store/temp/test_johnDD.zip" is not a directory. Assuming ISArchive file.
2017-04-24 08:50:10 INFO     data_set_manager.isa_tab_parser:974 run() - ISArchive extracted to "/tmp/tmpkLygx1/test_johnDD/".
2017-04-24 08:50:10 INFO     data_set_manager.isa_tab_parser:703 _create_investigation_file_section_model() - Column 1 in section ONTOLOGY SOURCE REFERENCE has no non-empty cells and was ignored.
2017-04-24 08:50:10 WARNING  data_set_m

drj11

My CV is available online at https://github.com/drj11/cv

Open Source has created an incredibly valuable ecosystem. So far, this ecosystem is software tools for professional programmers. I'm keen to see Open Source create value in the scientific community.

Life sciences are being revolutionised by a tsunami of data, personal omics being just one example. Using this data to deliver valuable services to society (without being crushed under the tsunami!) will involve computation and computing skills.

drj11

From a conversation with roryk about gemini and extasy on 2017-02-28

gemini does 2 things: 1) gather data from a bunch of sources to make a VCF file; and, 2) let's you query over that VCF.

The two things are separable.

So if we have a bunch of annotations, then if they are in a VCF file we can add them to Gemini's VCF using cvf2anno (which is scriptable in lua, yay!).

drj11

Dear Teen Vogue, attention Hanna Howard,

I think you should get more into coding.

Following, is an elaboration of that.

I am one of your readers (Twitter and Web). I doubt that I am a typical reader: I am a grumpy middle aged man who works as a programmer in a science lab in a university in the North of England.

drj11

bcbio for Dummies

(like me)

download template. This creates a directory (in the example below, the directory is my_dummy_dir), in which you will find a .yaml file.

bcbio_nextgen.py -w template illumina-rnaseq my_dummy_dir

(where is this documented?)