-
Notifications
You must be signed in to change notification settings - Fork 0
fall_2020_log
COB workshop:
http://ontology.buffalo.edu/bfo/SQU.pdf
https://docs.google.com/document/d/1LuUENHEwe0lKrghSpDJb8q8FUkBVakuaeZU5Z0OjorY/edit
https://docs.google.com/document/d/1cX9uImaE103MRyXJ1gGXn4KN-rzocldISuCGWQ-vBPw/edit
cob-data-demo from James Overton
COB Workshop 2020 drive folder need to finish watching day 1 part 2 chemistry material.
COB UO ticket: https://github.com/jamesaoverton/cob-data-demo/issues/1
Login for lytic UA netID and pass:
Use this: https://github.com/hurwitzlab/planet-microbe-functional-annotation/blob/master/singularity/recipe.def along with one of the hurwitz lab repo perhaps something called tacc-template that has a good skeleton by which to copy for the creation of a singularity image for the EBI pipeline that Matt M has now finished.
Links from NERC given from Mike Kittridge in this ENVO thread
https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/P01/
http://seadatanet.maris2.nl/bandit/browse_step.php
https://github.com/nvs-vocabs/P01
BODC presentation: https://github.com/nvs-vocabs/P01/blob/master/The_BODC_P01_PUV_semantic_model_Aug2019.pdf
physical parameter CV http://vocab.nerc.ac.uk/collection/S29/current/
chemical CV http://vocab.nerc.ac.uk/collection/S27/current/
Having issues on Mac, so I tried it on linux, which works.
git clone https://github.com/INCATools/ontology-development-kit.git
sudo docker pull obolibrary/odkfull
mv ~/.gitconfig/ ~/.gitconfig_backup_dir
vim ~/.gitconfig and paste in the following:
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
name = Kai Blumberg
email = [email protected]
now finally the odk example will run sudo ./seed-via-docker.sh -d po -d ro -d pato -u cmungall -t "Triffid Behavior ontology" triffo
Now to start BCODMO:
Make the file:
bcodmont.yaml and put it in ontology-development-kit/examples/bcodmo
id: bcodmont
title: BCODMO Ontology
github_org: BCODMO
repo: bcodmont
import_group:
products:
- id: ro
- id: pato
- id: envo
- id: iao
- id: obi
- id: uo
- id: uberon
sudo ./seed-via-docker.sh -C examples/bcodmo/bcodmont.yaml
####
NEXT STEPS:
0. Examine target/bcodmont and check it meets your expectations. If not blow it away and start again
1. Go to: https://github.com/new
2. The owner MUST be BCODMO. The Repository name MUST be bcodmont
3. Do not initialize with a README (you already have one)
4. Click Create
5. See the section under '…or push an existing repository from the command line'
E.g.:
cd target/bcodmont
git remote add origin git\@github.com:BCODMO/bcodmont.git
git push -u origin master
BE BOLD: you can always delete your repo and start again
modified from the …or push an existing repository from the command line Note you can't add a readme or license (probably .gitnore either) otherwise you won't get to here and there will be a merge conflict when you try to push the ODK created material to the new repo.
cd target/bcodmont
sudo git remote add origin https://github.com/BCODMO/bcodmont.git
sudo git branch -M main
sudo git push -u origin main
Had previously tried with the bcodmont.yaml to be:
id: bcodmont
title: BCODMO Ontology
github_org: BCODMO
repo: bcodmont
import_group:
products:
- id: ro
- id: pato
- id: envo
- id: iao
- id: obi
- id: uo
- id: bco
- id: pco
- id: uberon
- id: chebi
- id: ncbitaxon
but it won't work, chebi and probably ncbitaxon are too big and might time out, will have to add manually like I did for CDNO.
added
export PATH=~/software/FragGeneScan1.3:$PATH
export PATH=~/software/Trimmomatic-0.39:$PATH
export PATH=~/software/my_interproscan/interproscan-5.44-79.0:$PATH
export PATH=~/software/pear-0.9.11-linux-x86_64/bin:$PATH
export PATH=~/software/vsearch-2.14.2:$PATH
to .bashrc on my EBI atmosphere VM and did source .bashrc to always add them.
Run with: python3 pipeline/pipeline.py -c ./data/configs/config.txt
Have to change: in the pipeline.py
self.trim_executable_fp = os.environ.get('TRIMMOMATIC-0.39.JAR', default='/home/u29/mattmiller899/Trimmomatic-0.39/trimmomatic-0.39.jar') the default to: ~/software/Trimmomatic-0.39/trimmomatic-0.39.jar
From Matt M: about singularity https://sylabs.io/guides/3.6/user-guide/build_a_container.html#creating-writable-sandbox-directories
EBI's view to get the data e.g. https://www.ebi.ac.uk/ena/browser/view/SRR1185413
the bootstrap is technically the header. It's what defines the core operating system in the singularity image. A sample recipe would look like:
Bootstrap: docker
from: ubuntu:16.04
%setup
### First thing to run after base OS is installed, can execute commands on local host environment or in the container
### These commands have sudo privileges so it can be dangerous for the host environment. I usually don't have this section
%files
### This gets files from the host environment and puts them in the container
%post
### This is where you download files from the internet and install software, packages, etc.
%test
### Tests to run at the end of building
%environment
### Define environmental variables used at runtime (not during build time, if you need environmental variables during building you have to define them in post, but the post environmental variables will be available during runtime)
%runscript
### Put code you want to run when you do "singularity run my.simg arg1 arg2" or "./my.simg arg1 arg2. Receives the options as $* (single string) or $@ (quoted array)
echo "Hello, world"
For Ocelote, you can't use anything newer than Ubuntu v16.04 (idk about other linux flavors or Puma). For learning singularity, you can build a sandbox directory ("test_simg/") from the above template recipe ("test.def") and go into it and install stuff by
sudo singularity build --sandbox test_simg/ test.def
sudo singularity shell --writable test_simg/
Need to write a new ESIP session call.
ESIP sem harm: Call for Sessions WM21
2021 ESIP Winter Meeting Session Proposal Form (Responses)
from brandon: https://github.com/ESIPFed/sweet/pull/225
from bonnnie: phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
Original PATO repo, made a fork of it kaiiam/pato
From this post on keeping fork up to date run the following in the fork:
#add upstream
git remote add upstream https://github.com/pato-ontology/pato.git
#check
git remote -v
#update
git fetch upstream
# merge can maybe also do: git pull upstream master
git merge upstream/master
Pato editors readme edit the pato-edit.obo file. Their conventions are to:
-
put a
database_cross_referenceannotation property on the definition using type string. -
looks like they also add an id field with the curie of the purl (maybe an OBO thing)
-
Some terms have a
created_byI'll add my orcid -
Some terms have a
creation datewith iso date stamp.
Need to give myself an ID range will add it to my PR for issue https://github.com/pato-ontology/pato/issues/345. Will add the id range:
Datatype: idrange: 18
Annotations: allocatedto: "Kai Blumberg"
EquivalentTo: xsd:integer[> 85001 , <= 90000]
NERC meeting:
https://github.com/adamml/opm-owl
https://www.bodc.ac.uk/resources/vocabularies/vocabulary_builder/
https://www.bodc.ac.uk/resources/vocabularies/vocabulary_builder/matrix/
http://vocab.nerc.ac.uk/collection/S26/current/
https://www.bodc.ac.uk/resources/vocabularies/vocabulary_builder/bioentrf/
example the nerc term for atmosphere is https://vocab.nerc.ac.uk/collections/S21/current/S21S001
Meeting with James Overton.
DROID user page, droid github page Amazing automating even more and running validation on terms in a template. Keep an eye on this in future hopefully I can beta test it.
obook ontology examples blog, to which he'll add the new ENVO robot merge workflow. I should check these out.