{"id":65,"date":"2023-09-12T12:14:56","date_gmt":"2023-09-12T12:14:56","guid":{"rendered":"https:\/\/www.embl.org\/groups\/modis\/?page_id=65"},"modified":"2026-05-07T14:27:10","modified_gmt":"2026-05-07T14:27:10","slug":"data-analysis","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/modis\/data-analysis\/","title":{"rendered":"Data Analysis"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-3\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>While Galaxy is the most accessible and efficient when performing standard analyses, more advanced statistical modeling or visualization usually requires specialized code, which can be written and executed using R on our RStudio Server instance. <\/p>\n\n\n\n<p>Workflow modeling, with Galaxy and other Workflow Management System (WMS), to achieve better analysis automation and reproducibility is also in our area of expertise and we can provide advice and support to beginners-to-advanced researchers.<\/p>\n\n\n\n<div style=\"height:25px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-galaxy\" data-vf-js-location-nearest-activation-target=\"\">Galaxy<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-posit-workbench\" data-vf-js-location-nearest-activation-target=\"\">RStudio on JupyterHub<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-67019a31-ae08-439c-89ef-18f7046b54af\" data-vf-js-location-nearest-activation-target=\"\">WMS &amp; Support<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-7db7ac41-5197-4ea7-823d-501ba6c8fac3\" data-vf-js-location-nearest-activation-target=\"\">Super Computer &amp; Software<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-galaxy\"><h2 class=\"vf-u-sr-only\">Galaxy<\/h2>\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/galaxy.embl.de\/\" target=\"_blank\">Galaxy<\/a> is a web app that allows performing reproducible data analyses in a user-friendly graphical interface.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Accessibility<\/h4>\n\n\n\n<p>Everyone at EMBL has access to our Galaxy instance. Login happens with your EMBL credentials.<br>Galaxy can be used by anyone but reveals to be an incredible asset specifically for bench scientists with little computer knowledge, as it makes it easy to run the most commonly used bioinformatics software.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Bioinformatics software<\/h4>\n\n\n\n<p>A variety of bioinformatics tools are available in a few clicks. This includes the most famous NGS, proteomics, and image data software. More can be deployed on-demand when specific interest is raised to us, do not hesitate to contact us.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Computing is performed on our HPC cluster<\/h4>\n\n\n\n<p>Resource intensive jobs launched with Galaxy are automatically executed on on <a href=\"https:\/\/www.embl.org\/internal-information\/it-services\/scientific-computing-resources-heidelberg\/\">EMBL&#8217;s high-performance computing infrastucture<\/a> (maintained by ITS). This means no additional hassle for researcher who never used a HPC cluster before.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Data access with FAIR principles<\/h4>\n\n\n\n<p>A quota of <strong>200Gb<\/strong> is allocated to each user. We encourage users to download useful analysis results to their group share when they are produced, and we expect users clean and purge useless data from their history in order to recover disk space. <\/p>\n\n\n\n<p class=\"vf-u-text-color--red vf-text--body vf-text-body--2\">Galaxy is not to be used as storage and we cannot guaranty the data will be kept for long-term. <\/p>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h6 class=\"wp-block-heading\">Upload data<\/h6>\n\n\n\n<p>This is the quickest option, but <strong>we do not recommend it for bigger files<\/strong> and\/or files that are <strong>already stored on your group share<\/strong>, as this will unnecessarily hurt your quota and potentially duplicate data.<\/p>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h6 class=\"wp-block-heading\">Access your group share data<\/h6>\n\n\n\n<p class=\"vf-text--body vf-text-body--2\"><strong>The data available on your group share at <code>\/g\/&lt;groupname&gt;<\/code> can directly be linked to your Galaxy data library<\/strong>.<br>This is has to be done by an admin. To do so, please open a request with us, with the list of files that need to be made available. This avoid unnecessary data duplication, which saves your group resources (disk space and ?)<\/p>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h6 class=\"wp-block-heading\">From and to LabID<\/h6>\n\n\n\n<p>Connections have been established between our Galaxy instance and LabID, out data management platform. Datasets can be transferred from LabID to Galaxy in a few clicks (and without data duplication). Sending the data back from Galaxy to LabID is currently being beta testing. This allows to permanently store Galaxy&#8217;s analysis results and referencing it it lab notes, linking it to samples, annotations, protocols, and reagents, etc.<\/p>\n\n\n\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Get Support<\/h4>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<a href=\"https:\/\/training.galaxyproject.org\/\" target=\"_blank\">\n<button class=\"vf-button vf-button--secondary vf-button--sm\">Galaxy Training Network<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<a href=\"https:\/\/chat.embl.org\/embl\/channels\/galaxy\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Chat with the EMBL Galaxy community<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<a href=\"mailto:gbcs_request@embl.de?subject=%5BPosit%20Workbench%5D%20I%20need%20help!\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Email us<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" style=\"--vf-card__image--aspect-ratio: 16 \/ 9;\">\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/galaxy.embl.de\">\n      Galaxy@EMBL       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n                <p class=\"vf-card__text\">Local Galaxy instance<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/training.galaxyproject.org\/\">\n      Galaxy Training Network       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n                <p class=\"vf-card__text\"><p class=\"lead\">Collection of tutorials developed and maintained by the worldwide Galaxy community<\/p><\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/chat.embl.org\/embl\/channels\/galaxy\">\n      Galaxy Chat       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n                <p class=\"vf-card__text\">Internal chatroom for our Galaxy users, to get advice and troubleshoot issues<\/p>\n      <\/div>\n<\/article>\n\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-posit-workbench\"><h2 class=\"vf-u-sr-only\">RStudio on JupyterHub<\/h2>\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div style=\"height:15px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p>RStudio &#8211; sometimes now referred to as Posit\u2122 Workbench &#8211; is a powerful Integrated Development Environment for R, the go-to programming language for bioinformaticians and statistician aiming at extracting valuable information from experimental data.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Accessibility<\/h4>\n\n\n\n<p>Everyone at EMBL can access RStudio via JupyterHub (at <a href=\"https:\/\/jupyterhub.test.embl.de\/\">https:\/\/jupyterhub.embl.de<\/a>). Login happens with your EMBL credentials.<\/p>\n\n\n\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Get Support<\/h4>\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<a href=\"https:\/\/chat.embl.org\/embl\/channels\/rstudio-server\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Chat with the EMBL RStudio community<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<a href=\"mailto:gbcs_request@embl.de?subject=%5BRStudio%5D%20I%20need%20help!\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Email us<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div class=\"vf-grid | vf-grid__col-1\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-centered  size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"320\" height=\"113\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2024\/08\/RStudio_logo_flat.svg_.png\" alt=\"\" class=\"wp-image-5103\" style=\"width:300px\" srcset=\"https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2024\/08\/RStudio_logo_flat.svg_.png 320w, https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2024\/08\/RStudio_logo_flat.svg_-300x106.png 300w\" sizes=\"auto, (max-width: 320px) 100vw, 320px\" \/><\/figure>\n\n\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-centered  size-medium is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"300\" height=\"50\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2023\/10\/posit-workbench-logo-full-transp-300x50.png\" alt=\"\" class=\"wp-image-200\" style=\"width:300px\" srcset=\"https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2023\/10\/posit-workbench-logo-full-transp-300x50.png 300w, https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2023\/10\/posit-workbench-logo-full-transp-1024x169.png 1024w, https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2023\/10\/posit-workbench-logo-full-transp-768x127.png 768w, https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2023\/10\/posit-workbench-logo-full-transp-1536x254.png 1536w, https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2023\/10\/posit-workbench-logo-full-transp.png 1556w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/figure>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" style=\"--vf-card__image--aspect-ratio: 16 \/ 9;\">\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"http:\/\/upyterhub.embl.de\/\">\n      RStudio on JupyterHub @EMBL       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n                <p class=\"vf-card__text\">Local RStudio instance<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/chat.embl.org\/embl\/channels\/rstudio-server\">\n      RStudio Server Chat       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n                <p class=\"vf-card__text\">Internal chatroom for our RStudio users, to get advice and troubleshoot issues<\/p>\n      <\/div>\n<\/article>\n\n\n<\/div>\n<\/div>\n<\/div>\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-67019a31-ae08-439c-89ef-18f7046b54af\"><h2 class=\"vf-u-sr-only\">WMS &amp; Support<\/h2>\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div style=\"height:20px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p>To achieve better automation and reproducibility of analysis, we much encourage the usage of analysis workflows and Workflow Management Systems (WMS).<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Galaxy<\/h4>\n\n\n\n<div style=\"height:15px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h6 class=\"wp-block-heading has-regular-font-size\">Next Generation Sequencing (NGS) data analysis<\/h6>\n\n\n\n<p>We will assist less computer savvy colleagues in their <strong>standard NGS data analysis<\/strong> (RNA-seq, ChIP-seq, ATAC-seq, HiC, scRNA-seq\u2026) by providing ready-to-use Galaxy workflows. <br><strong>Non standard analysis<\/strong> workflows have to be developed by you, nevertheless we can teach you the basics of Galaxy so that you can assemble your own workflow in no time. <\/p>\n\n\n\n<p>Our expertise in other domain than NGS is limited, however we help you with assembling your own workflow.<\/p>\n\n\n\n<div style=\"height:15px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h6 class=\"wp-block-heading has-regular-font-size\">Training<\/h6>\n\n\n\n<p>MODIS have regularly been providing training internally, and the Galaxy Training Network provide <strong><a href=\"https:\/\/training.galaxyproject.org\/\">live material<\/a><\/strong> to learn by yourself. This covers a large area of domains, including sequencing, miscroscopy, proteomics, metabolomics, etc.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-inline-end  size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"170\" height=\"95\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/modis\/wp-content\/uploads\/2023\/10\/NEXTFLOWSNAKEMAKE-LOGO.png\" alt=\"\" class=\"wp-image-458\"\/><\/figure>\n\n\n\n<h4 class=\"wp-block-heading\">Command-line based WMS<\/h4>\n\n\n\n<p>For bioinformaticians proficient with command line tools, we advise looking into command-line based WMS. The most commonly used at EMBL are Nextflow and Snakemake*.<\/p>\n\n\n\n<div style=\"height:15px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p class=\"vf-text--body vf-text-body--4\">(*) We cannot recommend one WMS over another. Snakemake and Nextflow are both powerful tool, and other WMS also exist out there. Picking the right tool is a hot topic in life sciences, many aspects are to be considered and the choice ultimately is <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33630841\/\">up to you<\/a>. However we at MODIS do have a better expertise on Nextflow.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">(GB Unit) Custom analysis &amp; long-term collaboration<\/h4>\n\n\n\n<p>When your group is part of the GB Unit, we can provide further support and collaborate on workflow development. This for example can either mean developing a custom Galaxy or Nextflow workflow, or collaborating on the development of a Nextflow workflow with bioinformaticians in your group in order to teach them best practice of software development with git and of modular workflow development.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Get Support<\/h4>\n\n\n\n<a href=\"https:\/\/chat.embl.org\/embl\/channels\/nextflow\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Nextflow chat<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<a href=\"https:\/\/chat.embl.org\/embl\/channels\/snakemake\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Snakemake chat<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<a href=\"https:\/\/chat.embl.org\/embl\/channels\/galaxy\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Galaxy chat<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<a href=\"mailto:gbcs_request@embl.de?subject=%5BWorkflow%5D%20I%20need%20help!\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Email us<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-7db7ac41-5197-4ea7-823d-501ba6c8fac3\"><h2 class=\"vf-u-sr-only\">Super Computer &amp; Software<\/h2>\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div style=\"height:15px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p>We maintain a super computer named Seneca, which we use to run RStudio Server. This computer can be accessed <em>via<\/em> ssh and is connected to your group share. It can be used to run basic Unix commands and <strong>resource inexpensive<\/strong> processing.<\/p>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSpecifications<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<ul class=\"wp-block-list\">\n<li>Dell Power Edge R7425<\/li>\n\n\n\n<li><strong>64 cores<\/strong> capable of 128 concurrent threads (2x AMD EPYC 7601 2,20GHz\/2,7GHz, 32C\/64T, 64M Cache (180W) DDR4-2666)<\/li>\n\n\n\n<li><strong>2Tb RAM<\/strong> (32x 64GB LRDIMM, 2666MT\/s)<\/li>\n\n\n\n<li>3.2Tb local storage Flash Disk (<code>\/tmpdata<\/code>)<\/li>\n<\/ul>\n\n<\/div>\n<\/details>\n\n\n\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Accessibility<\/h4>\n\n\n\n<p>Everyone at EMBL has access to Seneca. Login happens remotely <em>via<\/em> ssh to <code>seneca.embl.de<\/code> (when <a href=\"https:\/\/www.embl.org\/internal-information\/it-services\/network-access-heidelberg\/\">connected to the EMBL network<\/a>). <\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Cluster access<\/h4>\n\n\n\n<p>Seneca is configured as a <strong>SLURM submit host<\/strong> and therefore can be used to submit cluster jobs like <code>login01.cluster.embl.de<\/code> or <code>login02.cluster.embl.de<\/code>. Find more information on the <a href=\"https:\/\/wiki.embl.de\/cluster\/Main_Page\">ITS Cluster Wiki<\/a>.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Software<\/h4>\n\n\n\n<p>The majority of software and their versions are handled with <a href=\"https:\/\/easybuild.io\/\">Easybuild<\/a>, the software framework used and maintained by ITS. Software is specifically compiled against the platform it&#8217;s running on and is therefore optimised. A <em>specific version<\/em> of a software &#8211; compiled by a specific toolchain &#8211; is referred to as an environment <strong>module<\/strong>. Modules are loaded in the user environment on demand, by the user themself, using the <code>module<\/code> command. Loading a given module does load all the needed software dependencies with it.<\/p>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nModules basics<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p>Easybuild builds software modules. Linux comes with the <a href=\"https:\/\/modules.readthedocs.io\/en\/latest\/module.html\"><code>module<\/code> command-line<\/a> tool to interact with modules (we use Lmod), and typically load them into your environment, list the existing and\/or loaded ones, etc.<\/p>\n\n\n\n<h6 class=\"wp-block-heading has-regular-font-size\">List available modules<\/h6>\n\n\n\n<ul class=\"wp-block-list\">\n<li class=\"has-regular-font-size\"><code>module avail<\/code> lists all modules.<\/li>\n\n\n\n<li class=\"has-regular-font-size\"><code>module avail &lt;string&gt;<\/code> lists all module with <code>&lt;string&gt;<\/code> in their name (case insensitive), <em>e.g.<\/em> <code>module avail python<\/code> returns Python and IPython modules, etc.<\/li>\n\n\n\n<li class=\"has-regular-font-size\"><code>module spider<\/code> and <code>module spider &lt;string&gt;<\/code> do a similar job.<\/li>\n<\/ul>\n\n\n\n<h6 class=\"wp-block-heading has-regular-font-size\">Load a module<\/h6>\n\n\n\n<ul class=\"wp-block-list\">\n<li class=\"has-regular-font-size\"><code>module load &lt;module_name&gt; [&lt;module2_name&gt; ...]<\/code> loads the given module(s), e.g. <code>module load Python\/3.10.8-GCCcore-12.2.0 SciPy-bundle\/2023.02-gfbf-2022b<\/code> loads both Python and SciPy. Find names with the avail or spider commands.<\/li>\n<\/ul>\n\n\n\n<p class=\"vf-text--body vf-text-body--3\">When possible, load matching toolchain versions, <em>i.e.<\/em> versions that have been compile with the same <a href=\"https:\/\/docs.easybuild.io\/common-toolchains\/#common_toolchains_overview\">toolchain<\/a>.<\/p>\n\n\n\n<p class=\"vf-text--body vf-text-body--4\" style=\"font-style:normal;font-weight:300\">NB 1: When loading multiple modules and hitting a dependency conflict, the last loaded module wins, i.e. the last module that needs the dependency dictates the loaded version of said dependency. <\/p>\n\n\n\n<h6 class=\"wp-block-heading has-regular-font-size\">List loaded modules<\/h6>\n\n\n\n<ul class=\"wp-block-list\">\n<li class=\"has-regular-font-size\"><code>module list<\/code> lists all the loaded module. <\/li>\n<\/ul>\n\n\n\n<p class=\"vf-text--body vf-text-body--3\">Even after explicitly loading a single module, the list may contain multiple module. This is because loading a module means loading the given one and all the module it depends on. For example loading <code>R-bundle-Bioconductor\/3.16-foss-2022b-R-4.2.2<\/code> effectively loads R, Bioconductor, as well as 123 other dependencies.<\/p>\n\n\n\n<h6 class=\"wp-block-heading has-regular-font-size\">Unload module(s)<\/h6>\n\n\n\n<p class=\"vf-text--body vf-text-body--3\"><code>module unload &lt;module_name&gt;<\/code> unloads a given module and all obsolete dependencies .<br><code>module purge<\/code> unloads all the loaded module.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nNote on installing new software<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<p class=\"vf-text--body vf-text-body--2\">You cannot install your own software with Easybuild<sup>*<\/sup>.<\/p>\n\n\n\n<p>When you identify a piece of software that is not available, you can request its install to <a href=\"mailto:gbcs_request@embl.de?subject=[Software Install] Request install of new software\">us<\/a> or to <a href=\"mailto:itsupport@embl.de?subject=[Software Install] Request install of new software\">IT Services<\/a>. On our side, installing should not take long, providing that either (1) an <a href=\"https:\/\/github.com\/easybuilders\/easybuild-easyconfigs\/tree\/develop\/easybuild\/easyconfigs\">official easybuild recipe<\/a> exists, or (2) that the install procedure is standard &amp; following best practices.<\/p>\n\n\n\n<a href=\"mailto:gbcs_request@embl.de?subject=%5BSoftware%20Install%5D%20Request%20install%20of%20new%20software\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary vf-button--sm\">Request software install<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n\n\n<div style=\"height:15px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p class=\"vf-text--body vf-text-body--3\">As an alternative, you may also use virtual environments managers (like conda) but we provide only limited support for them.<\/p>\n\n\n\n<p class=\"vf-text--body vf-text-body--5\">* Effectively you <em>could<\/em> maintain your own Easybuild install, but this is advanced usage and out of scope of this document<\/p>\n\n<\/div>\n<\/details>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h4 class=\"wp-block-heading\">Limitations and good practices<\/h4>\n\n\n\n<p class=\"vf-u-text-color--green vf-text--body vf-text-body--2\">The machine running RStudio Server is powerful but is a <strong>shared resources accessible by all EMBL scientists<\/strong>. Be mindful of others.<\/p>\n\n\n\n<p class=\"vf-text--body vf-text-body--2\"><strong>Do not run resource intensive jobs on this machine or they will be killed.<\/strong><\/p>\n\n\n\n<div style=\"height:100px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n<\/div><\/div>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-65","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/pages\/65","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/comments?post=65"}],"version-history":[{"count":90,"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/pages\/65\/revisions"}],"predecessor-version":[{"id":14037,"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/pages\/65\/revisions\/14037"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/media?parent=65"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/modis\/wp-json\/wp\/v2\/embl_taxonomy?post=65"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}