{"id":1298,"date":"2023-05-30T10:32:43","date_gmt":"2023-05-30T10:32:43","guid":{"rendered":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1298"},"modified":"2024-05-08T15:11:03","modified_gmt":"2024-05-08T15:11:03","slug":"culebront%e5%ae%89%e8%a3%9d%e7%ad%86%e8%a8%98","status":"publish","type":"post","link":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1298","title":{"rendered":"CulebrONT\u5b89\u88dd\u7b46\u8a18"},"content":{"rendered":"\n<p>\u57fa\u56e0\u9ad4\u6563\u5f48\u69cd\u5b9a\u5e8f\u7684\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u5f88\u591a\uff0c\u7531\u65bc\u6838\u9178\u5b9a\u5e8f\u7684\u6578\u64da\u6a23\u614b\u96a8\u8457\u79d1\u6280\u9032\u6b65\u4e0d\u65b7\u6539\u8b8a\uff0c\u600e\u6a23\u9078\u64c7\u9019\u4e9b\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u5176\u5be6\u662f\u500b\u5927\u554f\u984c\u3002\u6211\u5011\u4f86\u8a66\u8a66\u9019\u500bCulebrONT\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\uff0c\u9019\u7bc7\u662f\u6211\u5011\u7684\u5b89\u88dd\u7b46\u8a18\u3002<br>CulebrONT\u767c\u8868<a href=\"https:\/\/peercommunityjournal.org\/articles\/10.24072\/pcjournal.153\/\">\u539f\u6587\u51fa\u8655<\/a><\/p>\n\n\n\n<!--more-->\n\n\n\n<p>CulebrONT\u6587\u4ef6\u8aaa\u660e\uff1a<a rel=\"noreferrer noopener\" href=\"https:\/\/culebront-pipeline.readthedocs.io\/en\/latest\/index.html\" target=\"_blank\">https:\/\/culebront-pipeline.readthedocs.io\/en\/latest\/index.html<\/a><\/p>\n\n\n\n<p>\u5be6\u9a57\u5ba4\u7684Z2\u5de5\u4f5c\u7ad9\u4f5c\u696d\u7cfb\u7d71\u662fUbuntu\uff0c\u5df2\u7d93\u6709\u5b89\u88ddPython\u4e86\uff0c\u4f9d\u7167<a href=\"https:\/\/culebront-pipeline.readthedocs.io\/en\/latest\/index.html\">CulebrONT\u7684\u5b89\u88dd\u8aaa\u660e<\/a>\uff0c\u6211\u5011\u9084\u9700\u8981\u5148\u53e6\u5916\u5b89\u88dd\uff32\u8207Graphviz\uff0c\u4ee5\u4e0b\u662f\u7528SSH\u9060\u7aef\u767b\u5165\u9032\u884c\u5b89\u88dd\u7684\u904e\u7a0b\u8a18\u9304\uff1a<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">1. \u5b89\u88ddR<\/h2>\n\n\n\n<p>R: https:\/\/cran.r-project.org<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background\"><code># update indices\n$ sudo apt update -qq\n\n# install two helper packages we need\n$ sudo apt install --no-install-recommends software-properties-common dirmngr\n\n# add the signing key (by Michael Rutter) for these repos\n# To verify key, run gpg --show-keys \/etc\/apt\/trusted.gpg.d\/cran_ubuntu_key.asc \n# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9\n$ 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\n\n# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed\n$ sudo add-apt-repository \"deb https:\/\/cloud.r-project.org\/bin\/linux\/ubuntu $(lsb_release -cs)-cran40\/\"\n\n#installation\n$ sudo apt install --no-install-recommends r-base<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">2. \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\"><code>$ sudo apt install graphviz<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">3. \u7136\u5f8c\u5b89\u88ddCulebrONT\uff1a<\/h2>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background\"><code>$ python3 -m pip install culebrONT\nculebrONT --help\n\n#\u4ee5\u4e0b\u8981\u4e0b\u8f09\u8d85\u904e4G\u7684\u5167\u5bb9\u5594\n$ culebrONT install_local<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-large\"><a href=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"719\" src=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT-1024x719.jpg\" alt=\"\" class=\"wp-image-1299\" srcset=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT-1024x719.jpg 1024w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT-300x211.jpg 300w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT-768x539.jpg 768w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT-1536x1079.jpg 1536w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT-130x90.jpg 130w, https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2023\/05\/CulebrONT.jpg 1714w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">4. \u9084\u8981\u88dd<a href=\"https:\/\/github.com\/sylabs\/singularity\/releases\">Singularity<\/a>  <\/h2>\n\n\n\n<p>\u5176\u5be6\u6309\u7167\u8aaa\u660e\u6587\u4ef6\uff0c\u539f\u672c\u5230\u9019\u500b\u6b65\u9a5f\u5c31\u7b97\u88dd\u5b8c\u4e86\uff0c\u4f46\u662f\u4ed6\u6703\u8dd1\u51fa\u4e00\u500b\u300cThe singularity command has to be available in order to use singularity integration.\u300d\u7684\u932f\u8aa4\u8b66\u544a\u3002\u986f\u7136\u662f\u544a\u8a34\u6211\u5011\uff0cCulebrONT\u9084\u5f97\u7528\u5230Singularity\u9019\u500bcontainer platform\uff0c\u4f46\u6211\u5011&#8230;.\u9084\u6c92\u6709\u88dd\u9019\u500b\uff01\u6240\u4ee5\u4ee5\u4e0b\u5c31\u4f86\u5b89\u88dd\u4e00\u4e0bSingularityCE\uff1a<br><a href=\"https:\/\/docs.sylabs.io\/guides\/main\/user-guide\/quick_start.html#quick-installation-steps\">Singularity\u7684\u7db2\u7ad9<\/a>\u6709\u8a73\u7d30\u5b89\u88dd\u8aaa\u660e\uff1ahttps:\/\/docs.sylabs.io\/guides\/main\/user-guide\/quick_start.html#quick-installation-steps<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">4.1. \u9996\u5148\uff0c\u7cfb\u7d71\u88e1\u9762\u8981\u5148\u88dd\u4e0a\u4e00\u4e9blibraries\u9084\u6709\u4f9d\u8cf4\u7684\u958b\u767c\u5957\u4ef6\uff1a<\/h4>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background\"><code>$ sudo apt-get install -y    wget    build-essential    libseccomp-dev    libglib2.0-dev    pkg-config    squashfs-tools    cryptsetup    runc<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">4.2. \u5b89\u88dd<a href=\"https:\/\/go.dev\/dl\/\">GO<\/a>\uff1a<\/h4>\n\n\n\n<p>SingularityCE\u662f\u7528GO\u5beb\u7684\uff0c\u9700\u8981\u5b89\u88ddGO\u3002\u53ef\u5230https:\/\/go.dev\/dl\/ \u4e0b\u8f09\u5230Linux\u7684\u7248\u672c\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background\"><code>#\u7528wget\u4e0b\u8f09\n$ wget https:\/\/go.dev\/dl\/go1.20.4.linux-amd64.tar.gz\n#\u89e3\u58d3\u7e2e\n$ sudo tar -C \/usr\/local -xzvf go1.20.4.linux-amd64.tar.gz\n#\u628a\u74b0\u5883\u8b8a\u6578\u8a2d\u7d66\u5b83\n$ echo 'export PATH=\/usr\/local\/go\/bin:$PATH' &gt;&gt; ~\/.bashrc &amp;&amp; \\\n  source ~\/.bashrc<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">4.3. \u5230GitHub\u4e0b\u8f09SingularityCE 3.11.3\u7684Source Code\u56de\u4f86\uff0c\u89e3\u58d3\u7e2e\uff1a<\/h4>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background\"><code>#\u4e0b\u8f09\nwget https:\/\/github.com\/sylabs\/singularity\/releases\/download\/v3.11.3\/singularity-ce-3.11.3.tar.gz\n#\u89e3\u58d3\u7e2e\ntar -xzf singularity-ce-3.11.3.tar.gz<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">4.4. \u7de8\u8b6f\u8207\u5b89\u88ddSingularityCE<\/h4>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background\"><code>$ cd singularity-ce-3.11.3\n$ .\/mconfig &amp;&amp; \\\n    make -C builddir &amp;&amp; \\\n    sudo make -C builddir install<\/code><\/pre>\n\n\n\n<p>\u9019\u6a23SingularityCE\u5c31\u53ef\u4ee5\u7528\u4e86\uff0c\u99ac\u4e0a\u4f86\u6e2c\u8a66\u4e00\u4e0b\u770b\u770b\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u5099\u8a3bGo compiler not found (May 2024)<\/h2>\n\n\n\n<p>\u6709\u4e00\u6b21\u6211\u5011\u5728\u53e6\u5916\u4e00\u53f0Ubuntu\u5b89\u88dd\u9019\u500b\uff0c\u7d50\u679c\u5728Sigularity 3.6.3\u5b89\u88dd\u7684\u6642\u5019\u9047\u5230\u4e86\u554f\u984c\u3002\u72c0\u6cc1\u662f\u660e\u660e\u5df2\u7d93\u88dd\u597d\u4e86Go 1.20.4\uff0c\u4f46\u662fSigularity\u7684\u5b89\u88dd\u5361\u5728\u9019\u88e1\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-f11f09a097433ed5431b1bd884168649\"><code>checking: host Go compiler (at least version 1.17)... not found!<\/code><\/pre>\n\n\n\n<p>\u6211\u5011\u5728<a href=\"https:\/\/github.com\/apptainer\/singularity\/issues\/5099\">\u9019\u88e1<\/a>\u627e\u5230\u4e86\u89e3\u65b9\uff0c\u4ed6\u5011\u9047\u5230\u7684\u554f\u984c\u5927\u540c\u5c0f\u7570\uff0c\u800c\u4ed6\u5011\u7684\u89e3\u6cd5\u7a0d\u4f5c\u4fee\u6539\u53ef\u4ee5\u89e3\u6c7a\u9019\u500bGo compiler not found\u7684\u554f\u984c\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">5. CulebrONT\u6e2c\u8a66\u5305\u7684\u4e0b\u8f09\u8207\u6e2c\u8a66\uff1a<\/h2>\n\n\n\n<p><a href=\"https:\/\/culebront-pipeline.readthedocs.io\/en\/latest\/INSTALL.html#check-install\">\u8aaa\u660e\u6587\u4ef6<\/a>\u5beb\u8aaaCulebrONT\u6709\u63d0\u4f9b\u6e2c\u8a66\u5305\u53ef\u4ee5\u4f7f\u7528\uff0c\u6211\u5011\u7167\u8457\u628a\u4ed6\u6293\u56de\u4f86\u88dd\u5728test\u5e95\u4e0b<\/p>\n\n\n\n<pre class=\"wp-block-code has-white-color has-black-background-color has-text-color has-background\"><code>#\u9019\u6703\u4e0b\u8f09300\u591aMB\u7684\u6e2c\u8a66\u5305\u5230test\u88e1\u9762\n$ culebrONT test_install -d test<\/code><\/pre>\n\n\n\n<p>\u7136\u5f8c\u6e2c\u8a66\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\"><code>$ culebrONT run_local -t 8 -c test\/data_test_config.yaml --singularity-args \"--bind $HOME\"<\/code><\/pre>\n\n\n\n<p>\u6e2c\u8a66\u6210\u679c\u7684\u7d50\u679c\u6703\u653e\u5728FINAL_RESULTS\u5e95\u4e0b\uff0c\u662f\u500b\u6f02\u4eae\u7684html\u5831\u544a\uff0c\u7528\u7db2\u9801\u700f\u89bd\u5668\u53ef\u4ee5\u95b1\u8b80\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u57fa\u56e0\u9ad4\u6563\u5f48\u69cd\u5b9a\u5e8f\u7684\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u5f88\u591a\uff0c\u7531\u65bc\u6838\u9178\u5b9a\u5e8f\u7684\u6578\u64da\u6a23\u614b\u96a8\u8457\u79d1\u6280\u9032\u6b65\u4e0d\u65b7\u6539\u8b8a\uff0c\u600e\u6a23\u9078\u64c7\u9019\u4e9b\u751f\u7269\u8cc7\u8a0a\u5de5\u5177\u5176\u5be6\u662f\u500b\u5927\u554f\u984c\u3002\u6211\u5011\u4f86\u8a66\u8a66\u9019\u500bCulebrONT\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\uff0c\u9019\u7bc7\u662f\u6211\u5011\u7684\u5b89\u88dd\u7b46\u8a18\u3002CulebrONT\u767c\u8868\u539f\u6587\u51fa\u8655<\/p>\n","protected":false},"author":1,"featured_media":1696,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"colormag_page_container_layout":"no_sidebar_full_width","colormag_page_sidebar_layout":"no_sidebar","footnotes":""},"categories":[5],"tags":[15,14,18,20],"class_list":["post-1298","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-blog","tag-bioinformatics","tag-genomics","tag-linux","tag-nanopore"],"_links":{"self":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/1298","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1298"}],"version-history":[{"count":21,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/1298\/revisions"}],"predecessor-version":[{"id":1817,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/1298\/revisions\/1817"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/media\/1696"}],"wp:attachment":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1298"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1298"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1298"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}