diff options
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/INSTALL.md | 6 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part2.html | 127 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part2.org | 21 |
3 files changed, 90 insertions, 64 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 367b452..0367c63 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -107,3 +107,9 @@ And run from the data dir guix environment --ad-hoc virtuoso-ose -- virtuoso-t -f Visit http://localhost:8890/sparql + +To update the turtle files do + + guix environment -C guix --ad-hoc python python-requests raptor2 curl --network -- python3 ./scripts/update_virtuoso/check_for_updates.py cache.txt dba dba + +where dba is the default password. diff --git a/doc/blog/using-covid-19-pubseq-part2.html b/doc/blog/using-covid-19-pubseq-part2.html index 567980d..eff6fcd 100644 --- a/doc/blog/using-covid-19-pubseq-part2.html +++ b/doc/blog/using-covid-19-pubseq-part2.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-08-26 Wed 05:01 --> +<!-- 2020-11-10 Tue 05:08 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>COVID-19 PubSeq - Arvados</title> @@ -40,7 +40,7 @@ } pre.src { position: relative; - overflow: visible; + overflow: auto; padding-top: 1.2em; } pre.src:before { @@ -195,50 +195,26 @@ </style> <link rel="Blog stylesheet" type="text/css" href="blog.css" /> <script type="text/javascript"> -/* -@licstart The following is the entire license notice for the -JavaScript code in this tag. - -Copyright (C) 2012-2020 Free Software Foundation, Inc. - -The JavaScript code in this tag is free software: you can -redistribute it and/or modify it under the terms of the GNU -General Public License (GNU GPL) as published by the Free Software -Foundation, either version 3 of the License, or (at your option) -any later version. The code is distributed WITHOUT ANY WARRANTY; -without even the implied warranty of MERCHANTABILITY or FITNESS -FOR A PARTICULAR PURPOSE. See the GNU GPL for more details. - -As additional permission under GNU GPL version 3 section 7, you -may distribute non-source (e.g., minimized or compacted) forms of -that code without the copy of the GNU GPL normally required by -section 4, provided you include this license notice and a URL -through which recipients can access the Corresponding Source. - - -@licend The above is the entire license notice -for the JavaScript code in this tag. -*/ +// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain <!--/*--><![CDATA[/*><!--*/ - function CodeHighlightOn(elem, id) - { - var target = document.getElementById(id); - if(null != target) { - elem.cacheClassElem = elem.className; - elem.cacheClassTarget = target.className; - target.className = "code-highlighted"; - elem.className = "code-highlighted"; - } - } - function CodeHighlightOff(elem, id) - { - var target = document.getElementById(id); - if(elem.cacheClassElem) - elem.className = elem.cacheClassElem; - if(elem.cacheClassTarget) - target.className = elem.cacheClassTarget; - } -/*]]>*///--> + function CodeHighlightOn(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.classList.add("code-highlighted"); + target.classList.add("code-highlighted"); + } + } + function CodeHighlightOff(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.classList.remove("code-highlighted"); + target.classList.remove("code-highlighted"); + } + } + /*]]>*///--> +// @license-end </script> </head> <body> @@ -252,18 +228,18 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org6501d83">1. The Arvados Web Server</a></li> -<li><a href="#orgcb7854f">2. The Arvados file interface</a></li> -<li><a href="#orgc8c3ccd">3. The PubSeq Arvados shell</a></li> -<li><a href="#org028c1b4">4. Wiring up CWL</a></li> -<li><a href="#org7cdc8cc">5. Using the Arvados API</a></li> -<li><a href="#org5961211">6. Troubleshooting</a></li> +<li><a href="#org10ef830">1. The Arvados Web Server</a></li> +<li><a href="#orgb6a7a42">2. The Arvados file interface</a></li> +<li><a href="#org0c7b94e">3. The PubSeq Arvados shell</a></li> +<li><a href="#org756005d">4. Wiring up CWL</a></li> +<li><a href="#orgf30b46f">5. Using the Arvados API</a></li> +<li><a href="#org3af3122">6. Troubleshooting</a></li> </ul> </div> </div> -<div id="outline-container-org6501d83" class="outline-2"> -<h2 id="org6501d83"><span class="section-number-2">1</span> The Arvados Web Server</h2> +<div id="outline-container-org10ef830" class="outline-2"> +<h2 id="org10ef830"><span class="section-number-2">1</span> The Arvados Web Server</h2> <div class="outline-text-2" id="text-1"> <p> We are using Arvados to run common workflow language (CWL) pipelines. @@ -283,8 +259,8 @@ workflows and the output of analysis pipelines (here CWL workflows). </div> -<div id="outline-container-orgcb7854f" class="outline-2"> -<h2 id="orgcb7854f"><span class="section-number-2">2</span> The Arvados file interface</h2> +<div id="outline-container-orgb6a7a42" class="outline-2"> +<h2 id="orgb6a7a42"><span class="section-number-2">2</span> The Arvados file interface</h2> <div class="outline-text-2" id="text-2"> <p> Arvados has the web server, but it also has a REST API and associated @@ -361,8 +337,8 @@ arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839d </div> </div> -<div id="outline-container-orgc8c3ccd" class="outline-2"> -<h2 id="orgc8c3ccd"><span class="section-number-2">3</span> The PubSeq Arvados shell</h2> +<div id="outline-container-org0c7b94e" class="outline-2"> +<h2 id="org0c7b94e"><span class="section-number-2">3</span> The PubSeq Arvados shell</h2> <div class="outline-text-2" id="text-3"> <p> When you login to Arvados (you can request permission from us) it is @@ -414,11 +390,34 @@ the git repo and starts a new run calling into /data/pubseq/bh20-seq-resource/venv3/bin/bh20-seq-analyzer which is essentially <a href="https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L354">monitoring</a> for uploads. </p> + +<p> +On <code>run --help</code> +</p> + +<pre class="example" id="org93c3a8a"> +optional arguments: + -h, --help show this help message and exit + --uploader-project UPLOADER_PROJECT + --pangenome-analysis-project PANGENOME_ANALYSIS_PROJECT + --fastq-project FASTQ_PROJECT + --validated-project VALIDATED_PROJECT + --workflow-def-project WORKFLOW_DEF_PROJECT + --pangenome-workflow-uuid PANGENOME_WORKFLOW_UUID + --fastq-workflow-uuid FASTQ_WORKFLOW_UUID + --exclude-list EXCLUDE_LIST + --latest-result-collection LATEST_RESULT_COLLECTION + --kickoff + --no-start-analysis + --once + --print-status PRINT_STATUS + --revalidate +</pre> </div> </div> -<div id="outline-container-org028c1b4" class="outline-2"> -<h2 id="org028c1b4"><span class="section-number-2">4</span> Wiring up CWL</h2> +<div id="outline-container-org756005d" class="outline-2"> +<h2 id="org756005d"><span class="section-number-2">4</span> Wiring up CWL</h2> <div class="outline-text-2" id="text-4"> <p> In above script <code>bh20-seq-analyzer</code> you can see that the <a href="https://www.commonwl.org/">Common @@ -459,8 +458,8 @@ For more see <a href="https://hpc.guix.info/blog/2019/01/creating-a-reproducible </div> </div> -<div id="outline-container-org7cdc8cc" class="outline-2"> -<h2 id="org7cdc8cc"><span class="section-number-2">5</span> Using the Arvados API</h2> +<div id="outline-container-orgf30b46f" class="outline-2"> +<h2 id="orgf30b46f"><span class="section-number-2">5</span> Using the Arvados API</h2> <div class="outline-text-2" id="text-5"> <p> Arvados provides a rich API for accessing internals of the Cloud @@ -476,8 +475,8 @@ get a list of <a href="https://github.com/arvados/bh20-seq-resource/blob/2baa88b </div> </div> -<div id="outline-container-org5961211" class="outline-2"> -<h2 id="org5961211"><span class="section-number-2">6</span> Troubleshooting</h2> +<div id="outline-container-org3af3122" class="outline-2"> +<h2 id="org3af3122"><span class="section-number-2">6</span> Troubleshooting</h2> <div class="outline-text-2" id="text-6"> <p> When workflows have errors we should check the logs in Arvados. @@ -494,7 +493,7 @@ see what parts failed. </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-08-26 Wed 05:01</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-11-09 Mon 01:20</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org index 4b827f5..d7816ba 100644 --- a/doc/blog/using-covid-19-pubseq-part2.org +++ b/doc/blog/using-covid-19-pubseq-part2.org @@ -96,6 +96,27 @@ the git repo and starts a new run calling into /data/pubseq/bh20-seq-resource/venv3/bin/bh20-seq-analyzer which is essentially [[https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L354][monitoring]] for uploads. +On ~run --help~ + +#+begin_example +optional arguments: + -h, --help show this help message and exit + --uploader-project UPLOADER_PROJECT + --pangenome-analysis-project PANGENOME_ANALYSIS_PROJECT + --fastq-project FASTQ_PROJECT + --validated-project VALIDATED_PROJECT + --workflow-def-project WORKFLOW_DEF_PROJECT + --pangenome-workflow-uuid PANGENOME_WORKFLOW_UUID + --fastq-workflow-uuid FASTQ_WORKFLOW_UUID + --exclude-list EXCLUDE_LIST + --latest-result-collection LATEST_RESULT_COLLECTION + --kickoff + --no-start-analysis + --once + --print-status PRINT_STATUS + --revalidate +#+end_example + * Wiring up CWL In above script ~bh20-seq-analyzer~ you can see that the [[https://www.commonwl.org/][Common |