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Kai Blumberg edited this page Oct 7, 2020 · 24 revisions

09.01

COB workshop:

http://ontology.buffalo.edu/bfo/SQU.pdf

https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormallyFusedAnatomicalEntities.yaml

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

09.02

Login for lytic UA netID and pass:

ssh [email protected]


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.

10.05

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/

10.06

Create BCODMONT via ODK:

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.

EBI pipeline

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

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