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diff --git a/doc/web/download.html b/doc/web/download.html index 1d196a0..998c87b 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> -<!-- 2020-06-12 Fri 04:41 --> +<!-- 2020-08-24 Mon 03:08 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Download</title> @@ -247,34 +247,35 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<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> +<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> <ul> -<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> +<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> </ul> </li> -<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> +<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> <ul> -<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> +<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> </ul> </li> -<li><a href="#org49778b7">8. Source code</a></li> +<li><a href="#orga430457">8. Source code</a></li> +<li><a href="#org768f91e">9. Citing PubSeq</a></li> </ul> </div> </div> -<div id="outline-container-orgcd3d82f" class="outline-2"> -<h2 id="orgcd3d82f"><span class="section-number-2">1</span> Workflow runs</h2> +<div id="outline-container-orgc7d7db3" class="outline-2"> +<h2 id="orgc7d7db3"><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 @@ -285,8 +286,8 @@ is listed under <code>Data collections</code>. All current data is listed </div> </div> -<div id="outline-container-org9aff936" class="outline-2"> -<h2 id="org9aff936"><span class="section-number-2">2</span> FASTA files</h2> +<div id="outline-container-org3b6bb40" class="outline-2"> +<h2 id="org3b6bb40"><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 @@ -296,8 +297,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-orgc3e953c" class="outline-2"> -<h2 id="orgc3e953c"><span class="section-number-2">3</span> Metadata</h2> +<div id="outline-container-orgef20a06" class="outline-2"> +<h2 id="orgef20a06"><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 @@ -319,8 +320,8 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-orgc9c55c4" class="outline-2"> -<h2 id="orgc9c55c4"><span class="section-number-2">4</span> Pangenome</h2> +<div id="outline-container-orgaabb9da" class="outline-2"> +<h2 id="orgaabb9da"><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 @@ -328,8 +329,8 @@ Pangenome data is made available in multiple guises. Variation graphs </p> </div> -<div id="outline-container-org82c3ce9" class="outline-3"> -<h3 id="org82c3ce9"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> +<div id="outline-container-org1171db3" class="outline-3"> +<h3 id="org1171db3"><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 @@ -338,8 +339,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<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 id="outline-container-orgfc74439" class="outline-3"> +<h3 id="orgfc74439"><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 @@ -348,8 +349,8 @@ implementation. </div> </div> -<div id="outline-container-org8faf32f" class="outline-3"> -<h3 id="org8faf32f"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> +<div id="outline-container-orge6bb923" class="outline-3"> +<h3 id="orge6bb923"><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 @@ -360,8 +361,8 @@ graph can be downloaded from </div> -<div id="outline-container-org0c452f6" class="outline-3"> -<h3 id="org0c452f6"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> +<div id="outline-container-org5978f5c" class="outline-3"> +<h3 id="org5978f5c"><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 @@ -372,8 +373,8 @@ Pangenome browser. </div> </div> -<div id="outline-container-org4707094" class="outline-2"> -<h2 id="org4707094"><span class="section-number-2">5</span> Log of workflow output</h2> +<div id="outline-container-orgae23127" class="outline-2"> +<h2 id="orgae23127"><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. @@ -381,8 +382,8 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-orgd4d8f91" class="outline-2"> -<h2 id="orgd4d8f91"><span class="section-number-2">6</span> All files</h2> +<div id="outline-container-org88613e5" class="outline-2"> +<h2 id="org88613e5"><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> @@ -390,16 +391,16 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org237b3cf" class="outline-2"> -<h2 id="org237b3cf"><span class="section-number-2">7</span> Planned</h2> +<div id="outline-container-org97e0327" class="outline-2"> +<h2 id="org97e0327"><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-org66e03ac" class="outline-3"> -<h3 id="org66e03ac"><span class="section-number-3">7.1</span> Raw sequence data</h3> +<div id="outline-container-org35758f9" class="outline-3"> +<h3 id="org35758f9"><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>. @@ -407,8 +408,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track </div> </div> -<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 id="outline-container-orgab1c848" class="outline-3"> +<h3 id="orgab1c848"><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>. @@ -416,8 +417,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker </div> </div> -<div id="outline-container-orgaedc43e" class="outline-3"> -<h3 id="orgaedc43e"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> +<div id="outline-container-orgadb7ade" class="outline-3"> +<h3 id="orgadb7ade"><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>. @@ -425,8 +426,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track </div> </div> -<div id="outline-container-org19a6a11" class="outline-3"> -<h3 id="org19a6a11"><span class="section-number-3">7.4</span> Protein prediction</h3> +<div id="outline-container-org3ec62c4" class="outline-3"> +<h3 id="org3ec62c4"><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. @@ -435,8 +436,8 @@ We aim to make protein predictions available. </div> </div> -<div id="outline-container-org49778b7" class="outline-2"> -<h2 id="org49778b7"><span class="section-number-2">8</span> Source code</h2> +<div id="outline-container-orga430457" class="outline-2"> +<h2 id="orga430457"><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 @@ -445,9 +446,18 @@ from </p> </div> </div> + +<div id="outline-container-org768f91e" class="outline-2"> +<h2 id="org768f91e"><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>. +</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 2020-06-12 Fri 04:41</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 2020-08-24 Mon 03:07</small>. </div> </body> </html> |