bedtools intersect -abam path/to/input.bam -b path/to/regions.bed > out.bam
Michele Mattioni mattions
mattions
/ handycommands.md
Created
September 21, 2015 10:04
mattions
/ Exploring different distribution.ipynb
Created
July 30, 2013 14:32
Shapes and definition of some statistical PDFs, handy to do some modelling.
You can see the rendered version on nbviewer here: http://nbviewer.ipython.org/urls/gist.github.com/mattions/6113437/raw/c5468ea930d6960225d83e112d7f3d00d9c13398/Exploring+different+distribution.ipynb
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Retrieving the data from the INCLUDE FHIR Data via the FHIR_resource.
Quick help:
python fhir_trisomy_bridge.py --help
usage: fhir_trisomy_bridge.py [-h] --cavatica_token CAVATICA_TOKEN --cavatica_project CAVATICA_PROJECT
--include_fhir_authentication_cookie INCLUDE_FHIR_AUTHENTICATION_COOKIE
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| # SBFS Privileged helper script | |
| # Allow root to see projects. Needed if you want to use docker | |
| # | |
| # Note: export the $SBG_SBFS_MOUNT_POINT variable in your | |
| # .bashrc | |
| # | |
| # For Example: | |
| # export SBG_SBFS_MOUNT_POINT=~/sbfs_mount_point | |
| # Make sure the `~/sbfs_mount_point` directory exists | |
| # |
mattions
/ style.min.css
Created
January 13, 2015 09:47
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| /*! | |
| * Bootstrap v3.2.0 (http://getbootstrap.com) | |
| * Copyright 2011-2014 Twitter, Inc. | |
| * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) | |
| *//*! normalize.css v3.0.1 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background:0}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:cont |
mattions
/ parse_git.sh
Last active
December 7, 2020 10:54
parse_git function in bash which updates your prompt with the git branch if it is a git repo
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| function parse_git_dirty { | |
| [[ $(git status 2> /dev/null | tail -n1) != "nothing to commit, working tree clean" ]] && echo "*" | |
| } | |
| function parse_git_branch { | |
| git branch --no-color 2> /dev/null | sed -e '/^[^*]/d' -e "s/* \(.*\)/(\1$(parse_git_dirty))/" | |
| } | |
| export PS1='\u@\h \[\033[1;33m\]\w\[\033[0m\]$(parse_git_branch)$ ' |
mattions
/ quick_access_to_projects_via_bg.py
Last active
June 26, 2020 16:46
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| import sevenbridges as sbg | |
| c = sbg.Config(profile='cavatica') | |
| api = sbg.Api(config=c) | |
| bg = api.billing_groups.get(id='14bc19f2-6a6a-4a44-bb07-f86020dad9c0') | |
| breakdown = bg.breakdown() | |
| for project_breakdown in breakdown.project_breakdown: | |
| project_id_parsed = (project_breakdown.href.split("/")[-2:]) | |
| project_id = "/".join(project_id_parsed) | |
| print(project_id) |
mattions
/ setup.sh
Last active
October 25, 2018 14:25
— forked from fracasula/setup.sh
How to install Bluejeans on Ubuntu
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| sudo apt install alien -y | |
| sudo alien bluejeans_1.28.9-2_amd64.rpm # or whatever is the file you downloaded from the bluejeans website | |
| sudo dpkg -i bluejeans_1.28.9-2_amd64.deb | |
| cd /lib/x86_64-linux-gnu | |
| #sudo ln -s libudev.so libudev.so.0 | |
| sudo ln -s libudev.so.1 libudev.so.0 | |
| # now you can launch bluejeans | |
| /opt/bluejeans/bluejeans-bin |
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| # Launch the docker container of the latest st_viewer | |
| # Note: We are using the $SBG_SBFS_MOUNT_POINT variable | |
| # You can replace that with the actual path if you do not | |
| # want to use the env variable. Check the `sbfs-privileges.sh` | |
| # file for details. | |
| # | |
| # The mounted projects will be found at `/STDatasets` mount point | |
| # within the docker container | |
| xhost +local:root |
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