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Description

GDV is a fast and easy to use genome browser. The main goal is to provide a tool for biologist and bioanalysts who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.

Use

A production version is running on bbcf. You can log in if you have an account on tequila which is automatic if you have a university account in Switzerland. If not, we will provide soon a demo version available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.

Installation

pyGDV is written in python, so the recommended way of installing it (as all python modules) is throught a virtual environment. Here we put notes on installing virtualenv (will build your virtual environment) & virtualenvwrapper (will make it easier to work with virtualenv).

Please refers to the official documentation if something goes wrong.

Virtualenv

  1. Install devellopers packages (already done usually).

    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)

  2. Install virtualenv sudo easy_install virtualenv

Virtualenvwrapper

  1. Install python pip (package manager)

  2. Install vitualenvwrapper: pip install virtualenvwrapper

  3. Define the directory that will contains your environements export WORKON_HOME=/usr/local/env (add in .bashrc) mkdir $WORKON_HOME

  4. Execute virtualenwrapper.sh then source it source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)

  5. Create the virtual environement that will contains GDV mkvirtualenv --no-site-packages -p python2.6 pygdv

You can now enter the virtual env with workon pygdv and exit with deactivate

pyGDV

It's not mandatory to install pyGDV on a virtualenv but it's recommended.

-- DRAFT --

  1. Install git (do it throught your package manager)

  2. Go to the directory where you want to install pyGDV.

  3. Execute :

     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs clone libraries bbcflib (git), bein (git), track (git), gMiner (git) a script will soon be provided to install them at once

  5. Add them to the virtualenv

     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production cp development.ini production.ini

  7. enter info needed in production.ini

  8. cp who.ini.sample who.ini

  9. fill who.ini

  10. paster setup-app production.ini

  11. prefix your application if needed

  12. enter the ip of the proxy if needed

  13. run ``paster serve production.ini`

  14. configure worker in celeryconfig.py

  15. run workers : celeryd

Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.

Licence

Copyright BBCF.

http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch

About

A user friendly genome browser

gdv.epfl.ch

Resources

Readme
Activity
Custom properties

Stars

2 stars

Watchers

8 watching

Forks

1 fork
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
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btn.onmouseover = function() { this.style.opacity = '1'; };
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btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
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codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
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addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
GitHub - bbcf/pygdv: A user friendly genome browser · GitHub
Skip to content
BranchesTags
Repository files navigation
Description
GDV is a fast and easy to use genome browser.
The main goal is to provide a tool for biologist and bioanalysts
who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.
Use
A production version is running on bbcf.
You can log in if you have an account on tequila which is automatic if
you have a university account in Switzerland. If not, we will provide soon a demo version
available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.
Installation
pyGDV is written in python, so the recommended way of installing it (as all python modules)
is throught a virtual environment.
Here we put notes on installing virtualenv (will build your virtual environment)
& virtualenvwrapper (will make it easier to work with virtualenv).
Please refers to the official documentation if something goes wrong.
Virtualenv
  1. Install devellopers packages (already done usually).
    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)
  2. Install virtualenv
sudo easy_install virtualenv
Virtualenvwrapper
  1. Install python pip (package manager)
  2. Install vitualenvwrapper:
pip install virtualenvwrapper
  3. Define the directory that will contains your environements
export WORKON_HOME=/usr/local/env (add in .bashrc)
mkdir $WORKON_HOME
  4. Execute virtualenwrapper.sh then source it
source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)
  5. Create the virtual environement that will contains GDV
mkvirtualenv --no-site-packages -p python2.6 pygdv
You can now enter the virtual env with workon pygdv and exit with deactivate
pyGDV
It's not mandatory to install pyGDV on a virtualenv but it's recommended.
-- DRAFT --
  1. Install git (do it throught your package manager)
  2. Go to the directory where you want to install pyGDV.
  3. Execute :
     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs
clone libraries bbcflib (git), bein (git), track (git), gMiner (git)
a script will soon be provided to install them at once
  5. Add them to the virtualenv
     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production
cp development.ini production.ini
  7. enter info needed in production.ini
  8. cp who.ini.sample who.ini
  9. fill who.ini
  10. paster setup-app production.ini
  11. prefix your application if needed
  12. enter the ip of the proxy if needed
  13. run ``paster serve production.ini`
  14. configure worker in celeryconfig.py
  15. run workers : celeryd
Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.
Licence
Copyright BBCF.
http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch
About
A user friendly genome browser
gdv.epfl.ch
Resources
Readme
Activity
Custom properties
Stars
2 stars
Watchers
8 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - bbcf/pygdv: A user friendly genome browser · GitHub
Skip to content
BranchesTags
Repository files navigation
Description
GDV is a fast and easy to use genome browser.
The main goal is to provide a tool for biologist and bioanalysts
who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.
Use
A production version is running on bbcf.
You can log in if you have an account on tequila which is automatic if
you have a university account in Switzerland. If not, we will provide soon a demo version
available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.
Installation
pyGDV is written in python, so the recommended way of installing it (as all python modules)
is throught a virtual environment.
Here we put notes on installing virtualenv (will build your virtual environment)
& virtualenvwrapper (will make it easier to work with virtualenv).
Please refers to the official documentation if something goes wrong.
Virtualenv
  1. Install devellopers packages (already done usually).
    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)
  2. Install virtualenv
sudo easy_install virtualenv
Virtualenvwrapper
  1. Install python pip (package manager)
  2. Install vitualenvwrapper:
pip install virtualenvwrapper
  3. Define the directory that will contains your environements
export WORKON_HOME=/usr/local/env (add in .bashrc)
mkdir $WORKON_HOME
  4. Execute virtualenwrapper.sh then source it
source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)
  5. Create the virtual environement that will contains GDV
mkvirtualenv --no-site-packages -p python2.6 pygdv
You can now enter the virtual env with workon pygdv and exit with deactivate
pyGDV
It's not mandatory to install pyGDV on a virtualenv but it's recommended.
-- DRAFT --
  1. Install git (do it throught your package manager)
  2. Go to the directory where you want to install pyGDV.
  3. Execute :
     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs
clone libraries bbcflib (git), bein (git), track (git), gMiner (git)
a script will soon be provided to install them at once
  5. Add them to the virtualenv
     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production
cp development.ini production.ini
  7. enter info needed in production.ini
  8. cp who.ini.sample who.ini
  9. fill who.ini
  10. paster setup-app production.ini
  11. prefix your application if needed
  12. enter the ip of the proxy if needed
  13. run ``paster serve production.ini`
  14. configure worker in celeryconfig.py
  15. run workers : celeryd
Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.
Licence
Copyright BBCF.
http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch
About
A user friendly genome browser
gdv.epfl.ch
Resources
Readme
Activity
Custom properties
Stars
2 stars
Watchers
8 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - bbcf/pygdv: A user friendly genome browser · GitHub
Skip to content
BranchesTags
Repository files navigation
Description
GDV is a fast and easy to use genome browser.
The main goal is to provide a tool for biologist and bioanalysts
who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.
Use
A production version is running on bbcf.
You can log in if you have an account on tequila which is automatic if
you have a university account in Switzerland. If not, we will provide soon a demo version
available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.
Installation
pyGDV is written in python, so the recommended way of installing it (as all python modules)
is throught a virtual environment.
Here we put notes on installing virtualenv (will build your virtual environment)
& virtualenvwrapper (will make it easier to work with virtualenv).
Please refers to the official documentation if something goes wrong.
Virtualenv
  1. Install devellopers packages (already done usually).
    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)
  2. Install virtualenv
sudo easy_install virtualenv
Virtualenvwrapper
  1. Install python pip (package manager)
  2. Install vitualenvwrapper:
pip install virtualenvwrapper
  3. Define the directory that will contains your environements
export WORKON_HOME=/usr/local/env (add in .bashrc)
mkdir $WORKON_HOME
  4. Execute virtualenwrapper.sh then source it
source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)
  5. Create the virtual environement that will contains GDV
mkvirtualenv --no-site-packages -p python2.6 pygdv
You can now enter the virtual env with workon pygdv and exit with deactivate
pyGDV
It's not mandatory to install pyGDV on a virtualenv but it's recommended.
-- DRAFT --
  1. Install git (do it throught your package manager)
  2. Go to the directory where you want to install pyGDV.
  3. Execute :
     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs
clone libraries bbcflib (git), bein (git), track (git), gMiner (git)
a script will soon be provided to install them at once
  5. Add them to the virtualenv
     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production
cp development.ini production.ini
  7. enter info needed in production.ini
  8. cp who.ini.sample who.ini
  9. fill who.ini
  10. paster setup-app production.ini
  11. prefix your application if needed
  12. enter the ip of the proxy if needed
  13. run ``paster serve production.ini`
  14. configure worker in celeryconfig.py
  15. run workers : celeryd
Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.
Licence
Copyright BBCF.
http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch
About
A user friendly genome browser
gdv.epfl.ch
Resources
Readme
Activity
Custom properties
Stars
2 stars
Watchers
8 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - bbcf/pygdv: A user friendly genome browser · GitHub
Skip to content
BranchesTags
Repository files navigation
Description
GDV is a fast and easy to use genome browser.
The main goal is to provide a tool for biologist and bioanalysts
who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.
Use
A production version is running on bbcf.
You can log in if you have an account on tequila which is automatic if
you have a university account in Switzerland. If not, we will provide soon a demo version
available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.
Installation
pyGDV is written in python, so the recommended way of installing it (as all python modules)
is throught a virtual environment.
Here we put notes on installing virtualenv (will build your virtual environment)
& virtualenvwrapper (will make it easier to work with virtualenv).
Please refers to the official documentation if something goes wrong.
Virtualenv
  1. Install devellopers packages (already done usually).
    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)
  2. Install virtualenv
sudo easy_install virtualenv
Virtualenvwrapper
  1. Install python pip (package manager)
  2. Install vitualenvwrapper:
pip install virtualenvwrapper
  3. Define the directory that will contains your environements
export WORKON_HOME=/usr/local/env (add in .bashrc)
mkdir $WORKON_HOME
  4. Execute virtualenwrapper.sh then source it
source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)
  5. Create the virtual environement that will contains GDV
mkvirtualenv --no-site-packages -p python2.6 pygdv
You can now enter the virtual env with workon pygdv and exit with deactivate
pyGDV
It's not mandatory to install pyGDV on a virtualenv but it's recommended.
-- DRAFT --
  1. Install git (do it throught your package manager)
  2. Go to the directory where you want to install pyGDV.
  3. Execute :
     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs
clone libraries bbcflib (git), bein (git), track (git), gMiner (git)
a script will soon be provided to install them at once
  5. Add them to the virtualenv
     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production
cp development.ini production.ini
  7. enter info needed in production.ini
  8. cp who.ini.sample who.ini
  9. fill who.ini
  10. paster setup-app production.ini
  11. prefix your application if needed
  12. enter the ip of the proxy if needed
  13. run ``paster serve production.ini`
  14. configure worker in celeryconfig.py
  15. run workers : celeryd
Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.
Licence
Copyright BBCF.
http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch
About
A user friendly genome browser
gdv.epfl.ch
Resources
Readme
Activity
Custom properties
Stars
2 stars
Watchers
8 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - bbcf/pygdv: A user friendly genome browser · GitHub
Skip to content
BranchesTags
Repository files navigation
Description
GDV is a fast and easy to use genome browser.
The main goal is to provide a tool for biologist and bioanalysts
who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.
Use
A production version is running on bbcf.
You can log in if you have an account on tequila which is automatic if
you have a university account in Switzerland. If not, we will provide soon a demo version
available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.
Installation
pyGDV is written in python, so the recommended way of installing it (as all python modules)
is throught a virtual environment.
Here we put notes on installing virtualenv (will build your virtual environment)
& virtualenvwrapper (will make it easier to work with virtualenv).
Please refers to the official documentation if something goes wrong.
Virtualenv
  1. Install devellopers packages (already done usually).
    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)
  2. Install virtualenv
sudo easy_install virtualenv
Virtualenvwrapper
  1. Install python pip (package manager)
  2. Install vitualenvwrapper:
pip install virtualenvwrapper
  3. Define the directory that will contains your environements
export WORKON_HOME=/usr/local/env (add in .bashrc)
mkdir $WORKON_HOME
  4. Execute virtualenwrapper.sh then source it
source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)
  5. Create the virtual environement that will contains GDV
mkvirtualenv --no-site-packages -p python2.6 pygdv
You can now enter the virtual env with workon pygdv and exit with deactivate
pyGDV
It's not mandatory to install pyGDV on a virtualenv but it's recommended.
-- DRAFT --
  1. Install git (do it throught your package manager)
  2. Go to the directory where you want to install pyGDV.
  3. Execute :
     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs
clone libraries bbcflib (git), bein (git), track (git), gMiner (git)
a script will soon be provided to install them at once
  5. Add them to the virtualenv
     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production
cp development.ini production.ini
  7. enter info needed in production.ini
  8. cp who.ini.sample who.ini
  9. fill who.ini
  10. paster setup-app production.ini
  11. prefix your application if needed
  12. enter the ip of the proxy if needed
  13. run ``paster serve production.ini`
  14. configure worker in celeryconfig.py
  15. run workers : celeryd
Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.
Licence
Copyright BBCF.
http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch
About
A user friendly genome browser
gdv.epfl.ch
Resources
Readme
Activity
Custom properties
Stars
2 stars
Watchers
8 watching
Forks
1 fork
Report repository
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Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - bbcf/pygdv: A user friendly genome browser · GitHub
Skip to content
BranchesTags
Repository files navigation
Description
GDV is a fast and easy to use genome browser.
The main goal is to provide a tool for biologist and bioanalysts
who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.
Use
A production version is running on bbcf.
You can log in if you have an account on tequila which is automatic if
you have a university account in Switzerland. If not, we will provide soon a demo version
available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.
Installation
pyGDV is written in python, so the recommended way of installing it (as all python modules)
is throught a virtual environment.
Here we put notes on installing virtualenv (will build your virtual environment)
& virtualenvwrapper (will make it easier to work with virtualenv).
Please refers to the official documentation if something goes wrong.
Virtualenv
  1. Install devellopers packages (already done usually).
    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)
  2. Install virtualenv
sudo easy_install virtualenv
Virtualenvwrapper
  1. Install python pip (package manager)
  2. Install vitualenvwrapper:
pip install virtualenvwrapper
  3. Define the directory that will contains your environements
export WORKON_HOME=/usr/local/env (add in .bashrc)
mkdir $WORKON_HOME
  4. Execute virtualenwrapper.sh then source it
source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)
  5. Create the virtual environement that will contains GDV
mkvirtualenv --no-site-packages -p python2.6 pygdv
You can now enter the virtual env with workon pygdv and exit with deactivate
pyGDV
It's not mandatory to install pyGDV on a virtualenv but it's recommended.
-- DRAFT --
  1. Install git (do it throught your package manager)
  2. Go to the directory where you want to install pyGDV.
  3. Execute :
     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs
clone libraries bbcflib (git), bein (git), track (git), gMiner (git)
a script will soon be provided to install them at once
  5. Add them to the virtualenv
     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production
cp development.ini production.ini
  7. enter info needed in production.ini
  8. cp who.ini.sample who.ini
  9. fill who.ini
  10. paster setup-app production.ini
  11. prefix your application if needed
  12. enter the ip of the proxy if needed
  13. run ``paster serve production.ini`
  14. configure worker in celeryconfig.py
  15. run workers : celeryd
Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.
Licence
Copyright BBCF.
http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch
About
A user friendly genome browser
gdv.epfl.ch
Resources
Readme
Activity
Custom properties
Stars
2 stars
Watchers
8 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
GitHub - bbcf/pygdv: A user friendly genome browser · GitHub
Skip to content
BranchesTags
Repository files navigation
Description
GDV is a fast and easy to use genome browser.
The main goal is to provide a tool for biologist and bioanalysts
who wants to VISUALIZE and ANALYSE their data in an interactive and responding way.
Use
A production version is running on bbcf.
You can log in if you have an account on tequila which is automatic if
you have a university account in Switzerland. If not, we will provide soon a demo version
available for everybody. If you really wan't to test GDV, please sent a email to bbcf webmaster.
Installation
pyGDV is written in python, so the recommended way of installing it (as all python modules)
is throught a virtual environment.
Here we put notes on installing virtualenv (will build your virtual environment)
& virtualenvwrapper (will make it easier to work with virtualenv).
Please refers to the official documentation if something goes wrong.
Virtualenv
  1. Install devellopers packages (already done usually).
    • Xcode (MacOS)
    • python-dev & build-essential (Debian, Ubuntu)
    • python-devel (Fedor)
  2. Install virtualenv
sudo easy_install virtualenv
Virtualenvwrapper
  1. Install python pip (package manager)
  2. Install vitualenvwrapper:
pip install virtualenvwrapper
  3. Define the directory that will contains your environements
export WORKON_HOME=/usr/local/env (add in .bashrc)
mkdir $WORKON_HOME
  4. Execute virtualenwrapper.sh then source it
source /usr/local/bin/virtualenvwrapper.sh (add in .bashrc)
  5. Create the virtual environement that will contains GDV
mkvirtualenv --no-site-packages -p python2.6 pygdv
You can now enter the virtual env with workon pygdv and exit with deactivate
pyGDV
It's not mandatory to install pyGDV on a virtualenv but it's recommended.
-- DRAFT --
  1. Install git (do it throught your package manager)
  2. Go to the directory where you want to install pyGDV.
  3. Execute :
     git clone https://github.com/yjarosz/pygdv
cd pygdv
python setup.py install
easy_install celery
easy_install webob==1.1.1
easy_install numpy
easy_install matplotlib
pip install -U kombu-sqlalchemy

  4. Install bbcflibs
clone libraries bbcflib (git), bein (git), track (git), gMiner (git)
a script will soon be provided to install them at once
  5. Add them to the virtualenv
     add2virtualenv bbcflib
add2virtualenv track
add2virtualenv bein
add2virtualenv gMiner

  6. copy developement ini file to make it for production
cp development.ini production.ini
  7. enter info needed in production.ini
  8. cp who.ini.sample who.ini
  9. fill who.ini
  10. paster setup-app production.ini
  11. prefix your application if needed
  12. enter the ip of the proxy if needed
  13. run ``paster serve production.ini`
  14. configure worker in celeryconfig.py
  15. run workers : celeryd
Useful startup scripts are pygdv_ctl& celery_ctl. You should look at them.
Licence
Copyright BBCF.
http://bbcf.epfl.ch/
webmaster.bbcf@epfl.ch
About
A user friendly genome browser
gdv.epfl.ch
Resources
Readme
Activity
Custom properties
Stars
2 stars
Watchers
8 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages