{"id":1812,"date":"2024-08-27T08:45:32","date_gmt":"2024-08-27T08:45:32","guid":{"rendered":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1812"},"modified":"2024-09-01T13:02:09","modified_gmt":"2024-09-01T13:02:09","slug":"culebront%e5%ae%89%e8%a3%9d%e7%ad%86%e8%a8%98%e6%96%b0%ef%bc%89","status":"publish","type":"post","link":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1812","title":{"rendered":"CulebrONT\u5b89\u88dd\u7b46\u8a18(\u65b0\uff09"},"content":{"rendered":"\n<p>\u73fe\u5728\u62ff\u9577\u5e8f\u5217\u505a\u57fa\u56e0\u9ad4\u7684\u6563\u5f48\u69cd\u5b9a\u5e8f\u7d44\u88dd\uff0c\u53ef\u4ee5\u7528\u7684\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u771f\u7684\u5f88\u591a\u3002\u554f\u984c\u662f\uff0c\u9078\u7528\u600e\u6a23\u7684\u5de5\u5177\u7d44\u88dd\u6bd4\u8f03\u597d\uff1f<a href=\"https:\/\/culebront-pipeline.readthedocs.io\/en\/latest\/index.html\">\u9019\u500b<\/a>\u53eb\u505aculebrONT\u7684\u958b\u6e90Snakemake pipeline\u662f\u4e00\u500b\u5f88\u6709\u7528\u7684\u6771\u897f\uff0c\u4ed6\u53ef\u4ee5\u7528\u4f86\u904b\u884c\u5404\u7a2e\u7684\u6563\u5f48\u69cd\u5b9a\u5e8f\u7d44\u88dd\u7684\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u3001\u4fee\u6b63(polishing)\u3001\u751a\u81f3\u65bc(\u6709\u5fc5\u8981\u7684\u8a71)\u628a\u5e8f\u5217\u5708\u8d77\u4f86\u7b49\u7b49\uff0c\u5e6b\u52a9\u4f60\u9032\u884c\u5404\u7a2e\u65b9\u6848\u9593\u7684\u6bd4\u8f03\uff0c\u8b93\u4f7f\u7528\u8005\u53ef\u4ee5\u5efa\u69cb\u9069\u5408\u81ea\u5df1\u7684\u7406\u60f3\u5de5\u4f5c\u6d41\u7a0b\u3002\u4ee5\u4e0b\u662f\u6211\u5011\u5728\u820a\u7684Z600\u96fb\u8166\u5de5\u4f5c\u7ad9\u4e0a\u91cd\u65b0\u5b89\u88ddculebrONT\u7684\u7b46\u8a18\u3002<\/p>\n\n\n\n<p><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u5b89\u88dd\u4f5c\u696d\u7cfb\u7d71<\/h2>\n\n\n\n<p>\u6211\u5011\u9019\u53f0\u662f\u4fee\u4fee\u88dc\u88dc\u904e\u7684HP Z600\u8001\u96fb\u8166\u5de5\u4f5c\u7ad9\uff0c\u786c\u9ad4\u898f\u683c\u662fXeon E5620x2 8 cores 24GB DDR3-1333 ECC Registered RAM (4GB*6) 1TB SATA SSD Nvidia GTX 1080 8GB\u3002\u9996\u5148\u662f\u5b89\u88ddLinux\u4f5c\u696d\u7cfb\u7d71\uff0c\u6211\u5011\u8981\u57281TB\u7684SSD\u4e0a\u9762\u5b89\u88dd\u7684\u4f5c\u696d\u7cfb\u7d71\u662fUbuntu 22.04.4 LTS (Jammy Jellyfish)\uff0c\u6e96\u5099\u5de5\u4f5c\uff1a<\/p>\n\n\n\n<p>\u5148\u5f9e<a href=\"https:\/\/releases.ubuntu.com\/jammy\/\">\u5b98\u7db2\u4e0b\u8f09<\/a>\u5b83\u768464-bit PC (AMD64) Desktop Image iso (ubuntu-22.04.4-desktop-amd64.iso)\uff0c\u7136\u5f8c\u7528<a href=\"https:\/\/etcher.balena.io\">balena etcher<\/a>\u5beb\u5230USB flash disk\u4e0a (\u8d85\u904e5Gb\u7684\u5bb9\u91cf)\u3002<\/p>\n\n\n\n<p>\u7528\u505a\u597d\u7684USB flash disk\u958b\u6a5f\u9032\u884c\u5b89\u88dd\u3002\u5f9eGRUB\u9078\u55ae\u4e2d\uff0c\u9078\u64c7Try or Install Ubuntu\uff0c\u8a9e\u7cfb\u9078English\uff0cInstall type\u9078Normal Installation\uff0c\u6838\u53d6Download updates while installing Ubuntu\u4ee5\u53caInstall third-party software for graphics and Wi-Fi hardware and additional media formats\u3002<\/p>\n\n\n\n<p>\u4e0b\u4e00\u500b\u9078\u55ae\uff0c\u56e0\u70ba\u9019\u500bSSD\u88e1\u9762\u7684\u6771\u897f\u5df2\u7d93\u4e0d\u8981\u4e86\uff0c\u6211\u5011\u9078\u53d6Erase disk and install Ubuntu\u3002<\/p>\n\n\n\n<p>\u9078\u5730\u5340\u3001\u5efa\u7acb\u4f7f\u7528\u8005\u540d\u7a31\u5bc6\u78bc\u3002\u9032\u884c\u5b89\u88dd\u3002\u5b8c\u6210\u4e4b\u5f8c\uff0c\u91cd\u65b0\u958b\u6a5f\uff0c\u7cfb\u7d71\u6703\u63d0\u9192\u4f60\u53d6\u51faUSB flash disk\u3002<\/p>\n\n\n\n<p>\u7b2c\u4e00\u6b21\u958b\u6a5f\u9032\u5165Ubuntu Desktop\u4e4b\u5f8c\uff0c\u9996\u5148\u505a\u7cfb\u7d71\u66f4\u65b0\uff1a<\/p>\n\n\n\n<p>sudo apt-get update<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u5b89\u88ddR<\/h2>\n\n\n\n<p>\u95dc\u65bcR\u7684\u5b89\u88dd\uff0c\u53c3\u8003<a href=\"https:\/\/cran.r-project.org\">https:\/\/cran.r-project.org<\/a> \uff0c\u6b65\u9a5f\u5982\u4e0b\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-81f22b903912f49b1e42fb7d551cb2e6\"><code><em># update indices <\/em>\n<em>$ sudo apt update -qq <\/em>\n\n<em># install two helper packages we need <\/em>\n<em>$ sudo apt install --no-install-recommends software-properties-common dirmngr <\/em>\n<em># add the signing key (by Michael Rutter) for these repos <\/em>\n<em># To verify key, run gpg --show-keys \/etc\/apt\/trusted.gpg.d\/cran_ubuntu_key.asc <\/em>\n<em># Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9 <\/em>\n<em>$ wget -qO- https:\/\/cloud.r-project.org\/bin\/linux\/ubuntu\/marutter_pubkey.asc | sudo tee -a \/etc\/apt\/trusted.gpg.d\/cran_ubuntu_key.asc <\/em>\n\n<em># add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed <\/em>\n<em>$ sudo add-apt-repository \"deb https:\/\/cloud.r-project.org\/bin\/linux\/ubuntu $(lsb_release -cs)-cran40\/\" <\/em>\n\n<em>#installation <\/em>\n<em>$ sudo apt install --no-install-recommends r-base<\/em><\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u5b89\u88ddGraphviz<\/h2>\n\n\n\n<p>Graphviz: https:\/\/graphviz.org\/download\/<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-f1c7911398151dac4cf54e893a22d400\"><code><em>$ sudo apt install graphviz<\/em><\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u5b89\u88ddGO<\/h2>\n\n\n\n<p>\u53c3\u8003<a href=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-admin\/post.php?post=1664\">\u9019\u7bc7<\/a>\u7684\u4f5c\u6cd5<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-2e6e601df449d1aceffd6894af8a2c3c\"><code><code>sudo apt-get install -y build-essential libseccomp-dev pkg-config squashfs-tools cryptsetup<\/code>\n<code>export VERSION=1.13.15 OS=linux ARCH=amd64<\/code>\n<code>wget -O \/tmp\/go${VERSION}.${OS}-${ARCH}.tar.gz https:\/\/dl.google.com\/go\/go${VERSION}.${OS}-${ARCH}.tar.gz<\/code>\n<code>sudo tar -C \/usr\/local -xzf \/tmp\/go${VERSION}.${OS}-${ARCH}.tar.gz<\/code>\n<code>echo 'export GOPATH=${HOME}\/go' &gt;&gt; ~\/.bashrc<\/code>\n<code>echo 'export PATH=\/usr\/local\/go\/bin:${PATH}:${GOPATH}\/bin' &gt;&gt; ~\/.bashrc<\/code>\n<code>source ~\/.bashrc<\/code>\ncurl -sSfL https:\/\/raw.githubusercontent.com\/golangci\/golangci-lint\/master\/install.sh | sh -s -- -b $(go env GOPATH)\/bin <strong>v1.58.0<\/strong>\n<\/code><\/pre>\n\n\n\n<p>\u5275\u5efa\u4e00\u500b\u76ee\u9304\u7d50\u69cb\uff0c\u4ee5\u5c07Singularity\u7684\u539f\u59cb\u78bc\u653e\u5728\u6b63\u78ba\u7684\u4f4d\u7f6e\u3002\u7136\u5f8ccd\u5207\u63db\u5230Singularity\u539f\u59cb\u78bc\u7684\u76ee\u9304\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-24186023fbbc84a8480536fc52308de2\"><code><code>mkdir -p ${GOPATH}\/src\/github.com\/sylabs &amp;&amp; \\<\/code>\n<code>cd ${GOPATH}\/src\/github.com\/sylabs<\/code><\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u5b89\u88ddSingularity<\/h2>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-17cf9d227ac97baf44ad39746044a315\"><code>git clone --recurse-submodules https:\/\/github.com\/sylabs\/singularity.git\n<code>cd singularity<\/code>\ngit checkout v4.1.2\n\n\u7136\u5f8c\u7de8\u8b6f\n<code>cd ${GOPATH}\/src\/github.com\/sylabs\/singularity &amp;&amp; \\.\/mconfig &amp;&amp; \\cd .\/builddir &amp;&amp; \\make<\/code><\/code><\/pre>\n\n\n\n<p>\u4ee5\u4e0a\u6b65\u9a5f\u51fa\u73fe\u932f\u8aa4\uff0c\u767c\u73fe\u9700\u8981\u5148\u88ddgit\uff0c\u6240\u4ee5<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-bf5b2aab7a8f3677ee441f1426e80851\"><code>sudo apt install git<\/code><\/pre>\n\n\n\n<p>\u7136\u5f8c\u518d\u505a\u4e00\u6b21\u7de8\u8b6f\uff0c\u767c\u73fe\u9084\u9700\u8981autoconf, lib tool, glib-2.0, fuse, libfuse-dev\uff0c\u6240\u4ee5\u5148\u7528sudo apt-get install\u4ee5\u4e0a\u9019\u4e9b\u5957\u4ef6\uff0c\u7136\u5f8c\u518d\u91cd\u65b0\u7de8\u8b6f\u5c31\u53ef\u4ee5\u6210\u529f\u4e86\u3002<\/p>\n\n\n\n<p>\u5982\u679c\u4ee5\u4e0a\u90fd\u9806\u5229\u901a\u904e\uff0c\u90a3\u5c31\u662f\u6700\u5f8c\u4e00\u6b65\uff01\u5c07Singularity\u5b89\u88dd\u5230\u7cfb\u7d71\u4e2d\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-48f708ae8441f2185f7672711452f676\"><code><code>sudo make install<\/code><\/code><\/pre>\n\n\n\n<p>\u7528singularity version\u770b\u770b\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-44c1f5ca84b8c096d9eab167acc52af0\"><code>4.1.2<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u4e0b\u8f09\u8207\u5b89\u88ddculebrONT<\/h2>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-40c212dc3cc4f97a812b365fd1d36ae8\"><code>$ python3 -m pip install culebrONT\n$ culebrONT install_local<\/code><\/pre>\n\n\n\n<p>\u9019\u88e1\u767c\u73fe\u9700\u8981\u5148\u5b89\u88ddpip\uff0c\u6240\u4ee5<\/p>\n\n\n\n<p>sudo apt install python3-pip<\/p>\n\n\n\n<p>\u7136\u5f8c\u518d\u91cd\u505a\u4e00\u6b21python3 -m pip install &#8230;.<br>\u4ed6\u6703\u9700\u8981\u4e0b\u8f09\u8d85\u904e4GB\u7684\u5167\u5bb9\uff0c\u6240\u4ee5\u53ef\u4ee5\u5728\u9019\u88e1\u64fa\u8457\u3002(\u6700\u597d\u5927\u6e05\u65e9\u505a\u9019\u4ef6\u4e8b\uff0c\u7db2\u8def\u901f\u5ea6\u6bd4\u8f03\u5feb)<\/p>\n\n\n\n<p>\u7b49\u5f85&#8230;.. <\/p>\n\n\n\n<p>\u53e6\u5916\uff0c\u6211\u767c\u73fe\u9019\u500bUbuntu 22.04\u6709\u500b\u554f\u984c\uff0c\u5c31\u662f\u5b89\u88dd\u4e4b\u5f8c\u6211\u5c31\u4e00\u76f4\u627e\u4e0d\u5230\u5b83\u7684&#8221;Settings&#8221;<br>\u9019\u500b\u554f\u984c\u597d\u50cf\u65e9\u5c31\u6709\u4e0d\u5c11\u4eba\u9047\u5230\u904e\u4e86\uff0c\u89e3\u6c7a\u7684\u65b9\u6cd5\u5c31\u662f\u91cd\u65b0\u5b89\u88ddsettings\uff0c\u6211\u5011\u53e6\u5916\u958b\u4e00\u500bterminal:<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-247ae476b9a997acc3a39bf1df539578\"><code>sudo apt-get update &amp;&amp; sudo apt-get install --reinstall gnome-control-center<\/code><\/pre>\n\n\n\n<p>\u5c31\u53ef\u4ee5\u4e86\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u6e2c\u8a66<\/h2>\n\n\n\n<p>\u88dd\u597d\u4e4b\u5f8c\u53ef\u4ee5\u88dd\u6e2c\u8a66\u6578\u64da\u4f86\u8dd1\u770b\u770b\uff0c\u9996\u5148\u4e0b\u8f09\u6e2c\u8a66\u7528\u7684\u6578\u64da\u5230test\u8cc7\u6599\u593e\uff1a<\/p>\n\n\n\n<pre id=\"codecell5\" class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-1eca0e492771532af31b74ea8ea3a788\"><code>culebrONT test_install -d test<\/code><\/pre>\n\n\n\n<p>\u958b\u59cb\u6e2c\u8a66\uff1a<\/p>\n\n\n\n<pre id=\"codecell7\" class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-cf59644dd173339a28c5bc9f8730703a\"><code>culebrONT run_local -t 8 -c test\/data_test_config.yaml --singularity-args \"--bind $HOME\"<\/code><\/pre>\n\n\n\n<p>\u6211\u9019\u88e1test\u653e\u5728\/home\/onion\/\u5e95\u4e0b\uff0c\u6211\u7528\u7684\u662f\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-3d81fbabdd019c16efc10322583a172a\"><code>culebrONT run_local --threads 8 --singularity-args \"--bind $HOME\" --config \/home\/onion\/test\/data_test_config.yaml<\/code><\/pre>\n\n\n\n<p>\u8dd1\u4e0b\u53bb\u624d\u77e5\u9053\u9019\u53f0\u8001\u96fb\u8166\u771f\u7684\u597d\u6162\u597d\u6162\u311f&#8230;. \ud83d\ude42<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><a href=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/08\/culebrONT-test-run.png\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"576\" src=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/08\/culebrONT-test-run-1024x576.png\" alt=\"\" class=\"wp-image-1821\" srcset=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/08\/culebrONT-test-run-1024x576.png 1024w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/08\/culebrONT-test-run-300x169.png 300w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/08\/culebrONT-test-run-768x432.png 768w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/08\/culebrONT-test-run-1536x864.png 1536w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/08\/culebrONT-test-run.png 1920w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a><\/figure>\n\n\n\n<p>\u7d50\u8a9e\uff1a\u96fb\u8166\u786c\u9ad4\u8001\u820a\u4f3c\u4e4e\u771f\u7684\u662f\u8dd1\u4e0d\u52d5\u7684\u3002\u6211\u5011\u628a\u9019\u500b\u65b0\u5b89\u88dd\u597d\u7684SSD\u642c\u5230\u53e6\u4e00\u53f0\u96fb\u8166(Xeon E2236 32G RAM RTX4000)\u4e0a\u8dd1test data\u5c31OK\u4e86\uff01<\/p>\n\n\n\n<p>\u9644\u8a3b\uff1a\u9019\u6b21\u65b0\u5b89\u88dd\u7684Ubuntu 22.04\u4e0d\u77e5\u70ba\u4f55(\u6709\u4eba\u8aaa\u4e5f\u8a31apt-get\u66f4\u65b0\u5c31\u6703\u597d)\u6c92\u6709\u986f\u793a\u684c\u9762\u5716\u793a\uff0c\u4f46\u6211\u5011\u9019\u6a23\u89e3\u6c7a\u7684\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background has-link-color wp-elements-6918eb5b6f09d22e01fbe496bc7fa8b5\"><code>sudo apt install gnome-shell-extension-desktop-icons<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u73fe\u5728\u62ff\u9577\u5e8f\u5217\u505a\u57fa\u56e0\u9ad4\u7684\u6563\u5f48\u69cd\u5b9a\u5e8f\u7d44\u88dd\uff0c\u53ef\u4ee5\u7528\u7684\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u771f\u7684\u5f88\u591a\u3002\u554f\u984c\u662f\uff0c\u9078\u7528\u600e\u6a23\u7684\u5de5\u5177\u7d44\u88dd\u6bd4\u8f03\u597d\uff1f\u9019\u500b\u53eb\u505aculebrONT\u7684\u958b\u6e90Snakemake 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1080<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"colormag_page_container_layout":"default_layout","colormag_page_sidebar_layout":"default_layout","footnotes":""},"categories":[5],"tags":[15,18,20,28],"class_list":["post-1812","post","type-post","status-publish","format-standard","hentry","category-blog","tag-bioinformatics","tag-linux","tag-nanopore","tag-ubuntu"],"magazineBlocksPostFeaturedMedia":{"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"colormag-highlighted-post":false,"colormag-featured-post-medium":false,"colormag-featured-post-small":false,"colormag-featured-image":false,"colormag-default-news":false,"colormag-featured-image-large":false},"magazineBlocksPostAuthor":{"name":"onion","avatar":"https:\/\/secure.gravatar.com\/avatar\/a596197721c6296d27446d1377ed931e199d7d76ae4dedbebf95195b579de271?s=96&d=mm&r=g"},"magazineBlocksPostCommentsNumber":false,"magazineBlocksPostExcerpt":"\u73fe\u5728\u62ff\u9577\u5e8f\u5217\u505a\u57fa\u56e0\u9ad4\u7684\u6563\u5f48\u69cd\u5b9a\u5e8f\u7d44\u88dd\uff0c\u53ef\u4ee5\u7528\u7684\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u771f\u7684\u5f88\u591a\u3002\u554f\u984c\u662f\uff0c\u9078\u7528\u600e\u6a23\u7684\u5de5\u5177\u7d44\u88dd\u6bd4\u8f03\u597d\uff1f\u9019\u500b\u53eb\u505aculebrONT\u7684\u958b\u6e90Snakemake 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