diff options
Diffstat (limited to 'doc/web')
| -rw-r--r-- | doc/web/download.html | 172 | ||||
| -rw-r--r-- | doc/web/download.org | 2 |
2 files changed, 75 insertions, 99 deletions
diff --git a/doc/web/download.html b/doc/web/download.html index 998c87b..2c8b5f7 100644 --- a/doc/web/download.html +++ b/doc/web/download.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> -<!-- 2020-08-24 Mon 03:08 --> +<!-- 2020-11-05 Thu 05:26 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Download</title> @@ -40,7 +40,7 @@ } pre.src { position: relative; - overflow: visible; + overflow: auto; padding-top: 1.2em; } pre.src:before { @@ -194,50 +194,26 @@ /*]]>*/--> </style> <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> @@ -247,35 +223,35 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orgc7d7db3">1. Workflow runs</a></li> -<li><a href="#org3b6bb40">2. FASTA files</a></li> -<li><a href="#orgef20a06">3. Metadata</a></li> -<li><a href="#orgaabb9da">4. Pangenome</a> +<li><a href="#orgf894fd0">1. Workflow runs</a></li> +<li><a href="#org51b7162">2. FASTA files</a></li> +<li><a href="#org572ed1f">3. Metadata</a></li> +<li><a href="#org6b6b3d3">4. Pangenome</a> <ul> -<li><a href="#org1171db3">4.1. Pangenome GFA format</a></li> -<li><a href="#orgfc74439">4.2. Pangenome in ODGI format</a></li> -<li><a href="#orge6bb923">4.3. Pangenome RDF format</a></li> -<li><a href="#org5978f5c">4.4. Pangenome Browser format</a></li> +<li><a href="#org9f4caf2">4.1. Pangenome GFA format</a></li> +<li><a href="#org110286f">4.2. Pangenome in ODGI format</a></li> +<li><a href="#orgc83e017">4.3. Pangenome RDF format</a></li> +<li><a href="#org8b1948b">4.4. Pangenome Browser format</a></li> </ul> </li> -<li><a href="#orgae23127">5. Log of workflow output</a></li> -<li><a href="#org88613e5">6. All files</a></li> -<li><a href="#org97e0327">7. Planned</a> +<li><a href="#org3848ad3">5. Log of workflow output</a></li> +<li><a href="#org3ecd561">6. All files</a></li> +<li><a href="#orga83843e">7. Planned</a> <ul> -<li><a href="#org35758f9">7.1. Raw sequence data</a></li> -<li><a href="#orgab1c848">7.2. Multiple Sequence Alignment (MSA)</a></li> -<li><a href="#orgadb7ade">7.3. Phylogenetic tree</a></li> -<li><a href="#org3ec62c4">7.4. Protein prediction</a></li> +<li><a href="#orgcdeb8a1">7.1. Raw sequence data</a></li> +<li><a href="#org25b78b5">7.2. Multiple Sequence Alignment (MSA)</a></li> +<li><a href="#org02f524d">7.3. Phylogenetic tree</a></li> +<li><a href="#org78366fa">7.4. Protein prediction</a></li> </ul> </li> -<li><a href="#orga430457">8. Source code</a></li> -<li><a href="#org768f91e">9. Citing PubSeq</a></li> +<li><a href="#org3344c28">8. Source code</a></li> +<li><a href="#orgdd54c12">9. Citing PubSeq</a></li> </ul> </div> </div> -<div id="outline-container-orgc7d7db3" class="outline-2"> -<h2 id="orgc7d7db3"><span class="section-number-2">1</span> Workflow runs</h2> +<div id="outline-container-orgf894fd0" class="outline-2"> +<h2 id="orgf894fd0"><span class="section-number-2">1</span> Workflow runs</h2> <div class="outline-text-2" id="text-1"> <p> The last runs can be viewed <a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects">here</a>. If you click on a run you can see @@ -286,8 +262,8 @@ is listed under <code>Data collections</code>. All current data is listed </div> </div> -<div id="outline-container-org3b6bb40" class="outline-2"> -<h2 id="org3b6bb40"><span class="section-number-2">2</span> FASTA files</h2> +<div id="outline-container-org51b7162" class="outline-2"> +<h2 id="org51b7162"><span class="section-number-2">2</span> FASTA files</h2> <div class="outline-text-2" id="text-2"> <p> The <b>public sequence resource</b> provides all uploaded sequences as @@ -297,15 +273,15 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-orgef20a06" class="outline-2"> -<h2 id="orgef20a06"><span class="section-number-2">3</span> Metadata</h2> +<div id="outline-container-org572ed1f" class="outline-2"> +<h2 id="org572ed1f"><span class="section-number-2">3</span> Metadata</h2> <div class="outline-text-2" id="text-3"> <p> Metadata can be downloaded as <a href="https://www.w3.org/TR/turtle/">Turtle RDF</a> as a <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">mergedmetadat.ttl</a> which can be loaded into any RDF triple-store. We provide a Virtuoso SPARQL endpoint ourselves which can be queried from <a href="http://sparql.genenetwork.org/sparql/">http://sparql.genenetwork.org/sparql/</a>. Query examples can be found in -our <a href="https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org">BLOG</a>. +the <a href="https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org">DOCS</a> </p> <p> @@ -320,8 +296,8 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-orgaabb9da" class="outline-2"> -<h2 id="orgaabb9da"><span class="section-number-2">4</span> Pangenome</h2> +<div id="outline-container-org6b6b3d3" class="outline-2"> +<h2 id="org6b6b3d3"><span class="section-number-2">4</span> Pangenome</h2> <div class="outline-text-2" id="text-4"> <p> Pangenome data is made available in multiple guises. Variation graphs @@ -329,8 +305,8 @@ Pangenome data is made available in multiple guises. Variation graphs </p> </div> -<div id="outline-container-org1171db3" class="outline-3"> -<h3 id="org1171db3"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> +<div id="outline-container-org9f4caf2" class="outline-3"> +<h3 id="org9f4caf2"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> <div class="outline-text-3" id="text-4-1"> <p> <a href="https://github.com/GFA-spec/GFA-spec">GFA</a> is a standard for graphical fragment assembly and consumed @@ -339,8 +315,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<div id="outline-container-orgfc74439" class="outline-3"> -<h3 id="orgfc74439"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3> +<div id="outline-container-org110286f" class="outline-3"> +<h3 id="org110286f"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3> <div class="outline-text-3" id="text-4-2"> <p> <a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimised dynamic genome/graph @@ -349,8 +325,8 @@ implementation. </div> </div> -<div id="outline-container-orge6bb923" class="outline-3"> -<h3 id="orge6bb923"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> +<div id="outline-container-orgc83e017" class="outline-3"> +<h3 id="orgc83e017"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> <div class="outline-text-3" id="text-4-3"> <p> An RDF file that includes the sequences themselves in a variation @@ -361,8 +337,8 @@ graph can be downloaded from </div> -<div id="outline-container-org5978f5c" class="outline-3"> -<h3 id="org5978f5c"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> +<div id="outline-container-org8b1948b" class="outline-3"> +<h3 id="org8b1948b"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> <div class="outline-text-3" id="text-4-4"> <p> The many JSON files that are named as @@ -373,8 +349,8 @@ Pangenome browser. </div> </div> -<div id="outline-container-orgae23127" class="outline-2"> -<h2 id="orgae23127"><span class="section-number-2">5</span> Log of workflow output</h2> +<div id="outline-container-org3848ad3" class="outline-2"> +<h2 id="org3848ad3"><span class="section-number-2">5</span> Log of workflow output</h2> <div class="outline-text-2" id="text-5"> <p> Including in below link is a log file of the last workflow runs. @@ -382,8 +358,8 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org88613e5" class="outline-2"> -<h2 id="org88613e5"><span class="section-number-2">6</span> All files</h2> +<div id="outline-container-org3ecd561" class="outline-2"> +<h2 id="org3ecd561"><span class="section-number-2">6</span> All files</h2> <div class="outline-text-2" id="text-6"> <p> <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/</a> @@ -391,16 +367,16 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org97e0327" class="outline-2"> -<h2 id="org97e0327"><span class="section-number-2">7</span> Planned</h2> +<div id="outline-container-orga83843e" class="outline-2"> +<h2 id="orga83843e"><span class="section-number-2">7</span> Planned</h2> <div class="outline-text-2" id="text-7"> <p> We are planning the add the following output (see also </p> </div> -<div id="outline-container-org35758f9" class="outline-3"> -<h3 id="org35758f9"><span class="section-number-3">7.1</span> Raw sequence data</h3> +<div id="outline-container-orgcdeb8a1" class="outline-3"> +<h3 id="orgcdeb8a1"><span class="section-number-3">7.1</span> Raw sequence data</h3> <div class="outline-text-3" id="text-7-1"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq tracker</a> and <a href="https://github.com/arvados/bh20-seq-resource/issues/63">BAM tracker</a>. @@ -408,8 +384,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track </div> </div> -<div id="outline-container-orgab1c848" class="outline-3"> -<h3 id="orgab1c848"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3> +<div id="outline-container-org25b78b5" class="outline-3"> +<h3 id="org25b78b5"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3> <div class="outline-text-3" id="text-7-2"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>. @@ -417,8 +393,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker </div> </div> -<div id="outline-container-orgadb7ade" class="outline-3"> -<h3 id="orgadb7ade"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> +<div id="outline-container-org02f524d" class="outline-3"> +<h3 id="org02f524d"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> <div class="outline-text-3" id="text-7-3"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo tracker</a>. @@ -426,8 +402,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track </div> </div> -<div id="outline-container-org3ec62c4" class="outline-3"> -<h3 id="org3ec62c4"><span class="section-number-3">7.4</span> Protein prediction</h3> +<div id="outline-container-org78366fa" class="outline-3"> +<h3 id="org78366fa"><span class="section-number-3">7.4</span> Protein prediction</h3> <div class="outline-text-3" id="text-7-4"> <p> We aim to make protein predictions available. @@ -436,8 +412,8 @@ We aim to make protein predictions available. </div> </div> -<div id="outline-container-orga430457" class="outline-2"> -<h2 id="orga430457"><span class="section-number-2">8</span> Source code</h2> +<div id="outline-container-org3344c28" class="outline-2"> +<h2 id="org3344c28"><span class="section-number-2">8</span> Source code</h2> <div class="outline-text-2" id="text-8"> <p> All source code for this website and tooling is available @@ -447,8 +423,8 @@ from </div> </div> -<div id="outline-container-org768f91e" class="outline-2"> -<h2 id="org768f91e"><span class="section-number-2">9</span> Citing PubSeq</h2> +<div id="outline-container-orgdd54c12" class="outline-2"> +<h2 id="orgdd54c12"><span class="section-number-2">9</span> Citing PubSeq</h2> <div class="outline-text-2" id="text-9"> <p> See the <a href="./about">FAQ</a>. @@ -457,7 +433,7 @@ See the <a href="./about">FAQ</a>. </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 2020-08-24 Mon 03:07</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 2020-11-05 Thu 05:26</small>. </div> </body> </html> diff --git a/doc/web/download.org b/doc/web/download.org index a3f1949..44fbeb1 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -39,7 +39,7 @@ Metadata can be downloaded as [[https://www.w3.org/TR/turtle/][Turtle RDF]] as a can be loaded into any RDF triple-store. We provide a Virtuoso SPARQL endpoint ourselves which can be queried from http://sparql.genenetwork.org/sparql/. Query examples can be found in -our [[https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org][BLOG]]. +the [[https://github.com/arvados/bh20-seq-resource/blob/master/doc/blog/using-covid-19-pubseq-part1.org][DOCS]] The Swiss Institute of Bioinformatics has included this data in https://covid-19-sparql.expasy.org/ and made it part of [[https://www.uniprot.org/][Uniprot]]. |