Caprion data analysis

Welcome!

This repository/site is dedicated to protein/peptide quantitative trait analysis using the Caprion platform, which is organised chonologically/logistically into the following sections.

Pilot studies

• autoencoder
• gwas2
• Pilot studies

Analysis

• Protein analysis
• Peptide analysis
• Miscellaneous analysis

Additional information

• Caprion panel
• Notes

Local file/web browsing

A web-style navigation is furnised as follows,

cd /rds/project/rds-zuZwCZMsS0w/Caprion_proteomics/analysis
module load ceuadmin/edge
python3 -m http.server &
edge http://127.0.0.1:8000 &

where 8000 is a port number (pn).

In case the browser does not show, use

edge --user-data-dir=/tmp/edge http://127.0.0.1:8000 &

'/tmp/edge' directory in replace of ~/.config/microsoft-edge.

One could browse mirrors of two web sites as well as files,

1. Caprion site. This is from /site as above.
2. SRCF site. The mirror is within the following subdirectory: /srcf.
3. Colocalisation. See /json/coloc.html. Chromosomal positions are in hg19.
4. Multiprotein mapping isotopes, /dup/json/dup.htm
5. Supplementary tables.

To facilitate navigation, an index.html is created in place, so python3 -m http.server 8000 & starts a home page for 1-5 above.

In case pn is already in use, a different one can be chosen as follows,

export pn=8000
if lsof -i :${pn}; then
    echo "Port ${pn} is already in use' try another one."
else
    python3 -m http.server ${pn} &
    server_pid=$!
    edge http://127.0.0.1:${pn} &
fi

and pn can be released with kill $server_pid (can be checked with ps).

Non-CSD3 browser(s)

This approach seems less problematic with user-data-dir mentioned above. We can again set up tunneling from CSD3 with

python3 -m http.server 8000 &
hostname

Once succeeded, we establish the connection elsewhere.

ssh -4 -L 8080:127.0.0.1:8000 -fN jhz22@${hostname}.hpc.cam.ac.uk

where hostname from CSD3 and ${hostname} have to be the same. We can then browse http://127.0.0.1:8080.