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diff --git a/doc/web/download.html b/doc/web/download.html index 001b071..1d196a0 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> -<!-- 2020-05-30 Sat 10:40 --> +<!-- 2020-06-12 Fri 04:41 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Download</title> @@ -247,33 +247,34 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orgcde4e6b">1. Workflow runs</a></li> -<li><a href="#org1b46d7e">2. FASTA files</a></li> -<li><a href="#orgf2db570">3. Metadata</a></li> -<li><a href="#org9f89b24">4. Pangenome</a> +<li><a href="#orgcd3d82f">1. Workflow runs</a></li> +<li><a href="#org9aff936">2. FASTA files</a></li> +<li><a href="#orgc3e953c">3. Metadata</a></li> +<li><a href="#orgc9c55c4">4. Pangenome</a> <ul> -<li><a href="#org436ee36">4.1. Pangenome GFA format</a></li> -<li><a href="#org6cd667b">4.2. Pangenome in ODGI format</a></li> -<li><a href="#org220b6cb">4.3. Pangenome RDF format</a></li> -<li><a href="#org78f267a">4.4. Pangenome Browser format</a></li> +<li><a href="#org82c3ce9">4.1. Pangenome GFA format</a></li> +<li><a href="#orgf63e9f7">4.2. Pangenome in ODGI format</a></li> +<li><a href="#org8faf32f">4.3. Pangenome RDF format</a></li> +<li><a href="#org0c452f6">4.4. Pangenome Browser format</a></li> </ul> </li> -<li><a href="#org8cced34">5. Log of workflow output</a></li> -<li><a href="#org9d23c51">6. All files</a></li> -<li><a href="#org105d2d4">7. Planned</a> +<li><a href="#org4707094">5. Log of workflow output</a></li> +<li><a href="#orgd4d8f91">6. All files</a></li> +<li><a href="#org237b3cf">7. Planned</a> <ul> -<li><a href="#org52bb570">7.1. Raw sequence data</a></li> -<li><a href="#org68c178c">7.2. Multiple Sequence Alignment (MSA)</a></li> -<li><a href="#org9ccf15c">7.3. Phylogenetic tree</a></li> -<li><a href="#org31c2b68">7.4. Protein prediction</a></li> +<li><a href="#org66e03ac">7.1. Raw sequence data</a></li> +<li><a href="#orgdfae1b9">7.2. Multiple Sequence Alignment (MSA)</a></li> +<li><a href="#orgaedc43e">7.3. Phylogenetic tree</a></li> +<li><a href="#org19a6a11">7.4. Protein prediction</a></li> </ul> </li> +<li><a href="#org49778b7">8. Source code</a></li> </ul> </div> </div> -<div id="outline-container-orgcde4e6b" class="outline-2"> -<h2 id="orgcde4e6b"><span class="section-number-2">1</span> Workflow runs</h2> +<div id="outline-container-orgcd3d82f" class="outline-2"> +<h2 id="orgcd3d82f"><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 @@ -284,8 +285,8 @@ is listed under <code>Data collections</code>. All current data is listed </div> </div> -<div id="outline-container-org1b46d7e" class="outline-2"> -<h2 id="org1b46d7e"><span class="section-number-2">2</span> FASTA files</h2> +<div id="outline-container-org9aff936" class="outline-2"> +<h2 id="org9aff936"><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 @@ -295,8 +296,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-orgf2db570" class="outline-2"> -<h2 id="orgf2db570"><span class="section-number-2">3</span> Metadata</h2> +<div id="outline-container-orgc3e953c" class="outline-2"> +<h2 id="orgc3e953c"><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 @@ -318,8 +319,8 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-org9f89b24" class="outline-2"> -<h2 id="org9f89b24"><span class="section-number-2">4</span> Pangenome</h2> +<div id="outline-container-orgc9c55c4" class="outline-2"> +<h2 id="orgc9c55c4"><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 @@ -327,8 +328,8 @@ Pangenome data is made available in multiple guises. Variation graphs </p> </div> -<div id="outline-container-org436ee36" class="outline-3"> -<h3 id="org436ee36"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> +<div id="outline-container-org82c3ce9" class="outline-3"> +<h3 id="org82c3ce9"><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 @@ -337,8 +338,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<div id="outline-container-org6cd667b" class="outline-3"> -<h3 id="org6cd667b"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3> +<div id="outline-container-orgf63e9f7" class="outline-3"> +<h3 id="orgf63e9f7"><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 @@ -347,8 +348,8 @@ implementation. </div> </div> -<div id="outline-container-org220b6cb" class="outline-3"> -<h3 id="org220b6cb"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> +<div id="outline-container-org8faf32f" class="outline-3"> +<h3 id="org8faf32f"><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 @@ -359,8 +360,8 @@ graph can be downloaded from </div> -<div id="outline-container-org78f267a" class="outline-3"> -<h3 id="org78f267a"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> +<div id="outline-container-org0c452f6" class="outline-3"> +<h3 id="org0c452f6"><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 @@ -371,8 +372,8 @@ Pangenome browser. </div> </div> -<div id="outline-container-org8cced34" class="outline-2"> -<h2 id="org8cced34"><span class="section-number-2">5</span> Log of workflow output</h2> +<div id="outline-container-org4707094" class="outline-2"> +<h2 id="org4707094"><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. @@ -380,8 +381,8 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org9d23c51" class="outline-2"> -<h2 id="org9d23c51"><span class="section-number-2">6</span> All files</h2> +<div id="outline-container-orgd4d8f91" class="outline-2"> +<h2 id="orgd4d8f91"><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> @@ -389,16 +390,16 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org105d2d4" class="outline-2"> -<h2 id="org105d2d4"><span class="section-number-2">7</span> Planned</h2> +<div id="outline-container-org237b3cf" class="outline-2"> +<h2 id="org237b3cf"><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-org52bb570" class="outline-3"> -<h3 id="org52bb570"><span class="section-number-3">7.1</span> Raw sequence data</h3> +<div id="outline-container-org66e03ac" class="outline-3"> +<h3 id="org66e03ac"><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>. @@ -406,8 +407,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track </div> </div> -<div id="outline-container-org68c178c" class="outline-3"> -<h3 id="org68c178c"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3> +<div id="outline-container-orgdfae1b9" class="outline-3"> +<h3 id="orgdfae1b9"><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>. @@ -415,8 +416,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker </div> </div> -<div id="outline-container-org9ccf15c" class="outline-3"> -<h3 id="org9ccf15c"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> +<div id="outline-container-orgaedc43e" class="outline-3"> +<h3 id="orgaedc43e"><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>. @@ -424,8 +425,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track </div> </div> -<div id="outline-container-org31c2b68" class="outline-3"> -<h3 id="org31c2b68"><span class="section-number-3">7.4</span> Protein prediction</h3> +<div id="outline-container-org19a6a11" class="outline-3"> +<h3 id="org19a6a11"><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. @@ -433,9 +434,20 @@ We aim to make protein predictions available. </div> </div> </div> + +<div id="outline-container-org49778b7" class="outline-2"> +<h2 id="org49778b7"><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 +from +<a href="https://github.com/arvados/bh20-seq-resource">https://github.com/arvados/bh20-seq-resource</a> +</p> +</div> +</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 2020-05-30 Sat 10:40</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 2020-06-12 Fri 04:41</small>. </div> </body> </html> diff --git a/doc/web/download.org b/doc/web/download.org index da6a9a7..7614c60 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -17,6 +17,7 @@ - [[#multiple-sequence-alignment-msa][Multiple Sequence Alignment (MSA)]] - [[#phylogenetic-tree][Phylogenetic tree]] - [[#protein-prediction][Protein prediction]] + - [[#source-code][Source code]] * Workflow runs @@ -100,3 +101,9 @@ See [[https://github.com/arvados/bh20-seq-resource/issues/43][Phylo tracker]]. ** Protein prediction We aim to make protein predictions available. + +* Source code + +All source code for this website and tooling is available +from +https://github.com/arvados/bh20-seq-resource |