Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

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Docker image for Molgenis

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
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Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

About

Docker image for Molgenis

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

About

Docker image for Molgenis

Resources

Stars

0 stars

Watchers

0 watching

Forks

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

About

Docker image for Molgenis

Resources

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0 stars

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0 watching

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Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
Skip to content

Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

About

Docker image for Molgenis

Resources

Stars

0 stars

Watchers

0 watching

Forks

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

About

Docker image for Molgenis

Resources

Stars

0 stars

Watchers

0 watching

Forks

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

About

Docker image for Molgenis

Resources

Stars

0 stars

Watchers

0 watching

Forks

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
Skip to content

Repository files navigation

Docker

Docker images for MOLGENIS applications.

Requirements

  • Git

  • Docker

  • Navigate to http://localhost:8081/ in your browser and verify that the page cannot be found

  • Both the molgenis images and the elastic search image require a 'large' amount of memory. It is therefore advised to supply the docker engine with a minimum of 4g memory when using the docker-compose file. Alternatively tryout the experimental feature branch that makes use of the 'UseCGroupMemoryLimitForHeap' java option to dynamically constrain memory usage.

Linux

On Linux, increase the operating system limits on mmap counts by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf.

Installation

git clone https://github.com/molgenis/docker.git

cd docker/molgenis/8.1

Start MOLGENIS

docker-compose up

Navigate to http://localhost:8081/ in your browser.

Stop MOLGENIS

Ctrl-C in the terminal

Remove installation

docker-compose down
docker volume prune

Start new MOLGENIS

docker-compose down
docker volume prune
git pull origin master
docker-compose up --force-recreate

Override the MOLGENIS image you want to use

Edit the .env file or export the variables in shell.

Example for .env file:

REGISTRY=registry.molgenis.org/molgenis/molgenis-app
TAG=PR-8000-1

Example for exporting variables in shell:

export REGISTRY=registry.molgenis.org/molgenis/molgenis-app
export TAG=PR-8000-1 

About

Docker image for Molgenis

Resources

Stars

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0 watching

Forks

Releases

Packages

Contributors

Languages