{"id":1145,"date":"2022-03-30T10:31:12","date_gmt":"2022-03-30T08:31:12","guid":{"rendered":"https:\/\/bioinfo2.ugr.es\/srnatoolbox\/?page_id=1145"},"modified":"2022-03-30T10:31:12","modified_gmt":"2022-03-30T08:31:12","slug":"srnatoolbox-docker","status":"publish","type":"page","link":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/srnatoolbox-docker\/","title":{"rendered":"sRNAtoolbox Docker"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Getting started with sRNAtoolbox Docker<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">The sRNAtoolbox docker provides the user with a number of preinstalled programs like all sRNAtoolbox tools, Vienna package, bowtie, samtools etc. needed for common small RNA data analysis.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">First of all, Docker must be installed. To install Docker in Ubuntu and MacOS please do the following:<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">1- Install docker<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>sudo apt update\nsudo apt install docker.io\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">2- Start docker as a service<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>\tsudo systemctl start docker\n\tsudo systemctl enable docker\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">To install Docker Desktop in Windows please follow&nbsp;<a href=\"https:\/\/docs.docker.com\/docker-for-windows\/install\/\">these<\/a>&nbsp;instructions.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">sRNAtoolbox docker is hosted in Dockerhub so the first step is to pull the image from it:<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>sudo docker pull ugrbioinfo\/srnatoolbox:latest\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">After this, your sRNAtoolbox docker image is downloaded and now you can launch it:<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>sudo docker run --hostname sRNAtoolbox --name sRNAtoolbox --user srna --workdir \/home\/srna -it ugrbioinfo\/srnatoolbox:latest \/bin\/bash\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">Alternatively, if you want to start the container with shared folders:<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>sudo docker run --hostname sRNAtoolbox --name sRNAtoolbox --user srna --workdir \/home\/srna --mount type=bind,source=MACHINE_FOLDER,destination=\/shared\/shared_folder -it ugrbioinfo\/srnatoolbox:latest \/bin\/bash\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">After the first use you can exit the container by typing \u201cexit\u201d and stop the container with the following:<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>sudo docker stop sRNAtoolbox\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">For further uses:<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>sudo docker start sRNAtoolbox \nsudo docker exec -term=SCREEN -it sRNAtoolbox \/bin\/bash<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Getting started with sRNAtoolbox Docker The sRNAtoolbox docker provides the user with a number of preinstalled &hellip;<\/p>\n<p class=\"read-more\"> <a class=\"more-link\" href=\"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/srnatoolbox-docker\/\"> <span class=\"screen-reader-text\">sRNAtoolbox Docker<\/span> Read more \u2192<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1145","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/wp-json\/wp\/v2\/pages\/1145","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/wp-json\/wp\/v2\/comments?post=1145"}],"version-history":[{"count":0,"href":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/wp-json\/wp\/v2\/pages\/1145\/revisions"}],"wp:attachment":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/srnatoolbox\/wp-json\/wp\/v2\/media?parent=1145"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}