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diff --git a/doc/web/about.html b/doc/web/about.html index bad4bb1..c907e6c 100644 --- a/doc/web/about.html +++ b/doc/web/about.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> -<!-- 2020-05-28 Thu 08:40 --> +<!-- 2020-05-29 Fri 08:27 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>About/FAQ</title> @@ -247,29 +247,29 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org43f7738">1. What is the 'public sequence resource' about?</a></li> -<li><a href="#orgde86ccd">2. Who created the public sequence resource?</a></li> -<li><a href="#orgdd37e45">3. How does the public sequence resource compare to other data resources?</a></li> -<li><a href="#org9edb5aa">4. Why should I upload my data here?</a></li> -<li><a href="#orgfbf8cae">5. Why should I not upload by data here?</a></li> -<li><a href="#org847ae99">6. How does the public sequence resource work?</a></li> -<li><a href="#orgf5b82cd">7. Who uses the public sequence resource?</a></li> -<li><a href="#orgb98ff9a">8. Is this about open data?</a></li> -<li><a href="#org1bd01df">9. Is this about free software?</a></li> -<li><a href="#org9b933c4">10. How do I upload raw data?</a></li> -<li><a href="#org3425b34">11. How do I change metadata?</a></li> -<li><a href="#org7ef551b">12. How do I change the work flows?</a></li> -<li><a href="#org2bdd0eb">13. How do I change the source code?</a></li> -<li><a href="#org0468035">14. Should I choose CC-BY or CC0?</a></li> -<li><a href="#org246712c">15. How do I deal with private data and privacy?</a></li> -<li><a href="#org29eb659">16. How do I communicate with you?</a></li> -<li><a href="#orgce9d1ee">17. Who are the sponsors?</a></li> +<li><a href="#org783b5e9">1. What is the 'public sequence resource' about?</a></li> +<li><a href="#org2c0bcfd">2. Who created the public sequence resource?</a></li> +<li><a href="#org34070d3">3. How does the public sequence resource compare to other data resources?</a></li> +<li><a href="#org64a9493">4. Why should I upload my data here?</a></li> +<li><a href="#orgf898e7f">5. Why should I not upload by data here?</a></li> +<li><a href="#org828e164">6. How does the public sequence resource work?</a></li> +<li><a href="#org7b0d03f">7. Who uses the public sequence resource?</a></li> +<li><a href="#org31aaf23">8. Is this about open data?</a></li> +<li><a href="#orgb376b6c">9. Is this about free software?</a></li> +<li><a href="#orgf19cd96">10. How do I upload raw data?</a></li> +<li><a href="#orgebfed00">11. How do I change metadata?</a></li> +<li><a href="#orge2aecf8">12. How do I change the work flows?</a></li> +<li><a href="#orgd45b3bc">13. How do I change the source code?</a></li> +<li><a href="#org2bb9455">14. Should I choose CC-BY or CC0?</a></li> +<li><a href="#org62bf23f">15. How do I deal with private data and privacy?</a></li> +<li><a href="#org40c6da0">16. How do I communicate with you?</a></li> +<li><a href="#org1f27c44">17. Who are the sponsors?</a></li> </ul> </div> </div> -<div id="outline-container-org43f7738" class="outline-2"> -<h2 id="org43f7738"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<div id="outline-container-org783b5e9" class="outline-2"> +<h2 id="org783b5e9"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> <div class="outline-text-2" id="text-1"> <p> The <b>public sequence resource</b> aims to provide a generic and useful @@ -280,8 +280,8 @@ sequence comparison and protein prediction. </div> </div> -<div id="outline-container-orgde86ccd" class="outline-2"> -<h2 id="orgde86ccd"><span class="section-number-2">2</span> Who created the public sequence resource?</h2> +<div id="outline-container-org2c0bcfd" class="outline-2"> +<h2 id="org2c0bcfd"><span class="section-number-2">2</span> Who created the public sequence resource?</h2> <div class="outline-text-2" id="text-2"> <p> The <b>public sequence resource</b> is an initiative by <a href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformatics</a> and @@ -301,8 +301,8 @@ wrangling experts. Thank you everyone! </div> </div> -<div id="outline-container-orgdd37e45" class="outline-2"> -<h2 id="orgdd37e45"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2> +<div id="outline-container-org34070d3" class="outline-2"> +<h2 id="org34070d3"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2> <div class="outline-text-2" id="text-3"> <p> The short version is that we use state-of-the-art practices in @@ -321,8 +321,8 @@ public resources, including GISAID. </div> </div> -<div id="outline-container-org9edb5aa" class="outline-2"> -<h2 id="org9edb5aa"><span class="section-number-2">4</span> Why should I upload my data here?</h2> +<div id="outline-container-org64a9493" class="outline-2"> +<h2 id="org64a9493"><span class="section-number-2">4</span> Why should I upload my data here?</h2> <div class="outline-text-2" id="text-4"> <ol class="org-ol"> <li>We champion truly shareable data without licensing restrictions - with proper @@ -332,6 +332,8 @@ attribution</li> for bulk uploads</li> <li>We provide a live SPARQL end-point for all metadata</li> <li>We provide free data analysis and sequence comparison triggered on data upload</li> +<li>We do real work for you, with this <a href="https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">link</a> you can see the last +run took 5.5 hours!</li> <li>We provide free downloads of all computed output</li> <li>There is no need to set up pipelines and/or compute clusters</li> <li>All workflows get triggered on uploading a new sequence</li> @@ -351,8 +353,8 @@ multiple resources. </div> </div> -<div id="outline-container-orgfbf8cae" class="outline-2"> -<h2 id="orgfbf8cae"><span class="section-number-2">5</span> Why should I not upload by data here?</h2> +<div id="outline-container-orgf898e7f" class="outline-2"> +<h2 id="orgf898e7f"><span class="section-number-2">5</span> Why should I not upload by data here?</h2> <div class="outline-text-2" id="text-5"> <p> Funny question. There are only good reasons to upload your data here @@ -374,8 +376,8 @@ for bulk uploads! </div> </div> -<div id="outline-container-org847ae99" class="outline-2"> -<h2 id="org847ae99"><span class="section-number-2">6</span> How does the public sequence resource work?</h2> +<div id="outline-container-org828e164" class="outline-2"> +<h2 id="org828e164"><span class="section-number-2">6</span> How does the public sequence resource work?</h2> <div class="outline-text-2" id="text-6"> <p> On uploading a sequence with metadata it will automatically be @@ -386,8 +388,8 @@ using workflows from the High Performance Open Biology Lab defined </div> </div> -<div id="outline-container-orgf5b82cd" class="outline-2"> -<h2 id="orgf5b82cd"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2> +<div id="outline-container-org7b0d03f" class="outline-2"> +<h2 id="org7b0d03f"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2> <div class="outline-text-2" id="text-7"> <p> The Swiss Institute of Bioinformatics has included this data in @@ -401,8 +403,8 @@ drug development. </div> </div> -<div id="outline-container-orgb98ff9a" class="outline-2"> -<h2 id="orgb98ff9a"><span class="section-number-2">8</span> Is this about open data?</h2> +<div id="outline-container-org31aaf23" class="outline-2"> +<h2 id="org31aaf23"><span class="section-number-2">8</span> Is this about open data?</h2> <div class="outline-text-2" id="text-8"> <p> All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0 attribution license</a> @@ -412,8 +414,8 @@ data and store it for further processing. </div> </div> -<div id="outline-container-org1bd01df" class="outline-2"> -<h2 id="org1bd01df"><span class="section-number-2">9</span> Is this about free software?</h2> +<div id="outline-container-orgb376b6c" class="outline-2"> +<h2 id="orgb376b6c"><span class="section-number-2">9</span> Is this about free software?</h2> <div class="outline-text-2" id="text-9"> <p> Absolutely. Free software allows for fully reproducible pipelines. You @@ -422,8 +424,8 @@ can take our workflows and data and run it elsewhere! </div> </div> -<div id="outline-container-org9b933c4" class="outline-2"> -<h2 id="org9b933c4"><span class="section-number-2">10</span> How do I upload raw data?</h2> +<div id="outline-container-orgf19cd96" class="outline-2"> +<h2 id="orgf19cd96"><span class="section-number-2">10</span> How do I upload raw data?</h2> <div class="outline-text-2" id="text-10"> <p> We are preparing raw sequence data pipelines (fastq and BAM). The @@ -438,8 +440,8 @@ assembly variations into consideration. This is all work in progress. </div> </div> -<div id="outline-container-org3425b34" class="outline-2"> -<h2 id="org3425b34"><span class="section-number-2">11</span> How do I change metadata?</h2> +<div id="outline-container-orgebfed00" class="outline-2"> +<h2 id="orgebfed00"><span class="section-number-2">11</span> How do I change metadata?</h2> <div class="outline-text-2" id="text-11"> <p> See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>! @@ -447,8 +449,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<div id="outline-container-org7ef551b" class="outline-2"> -<h2 id="org7ef551b"><span class="section-number-2">12</span> How do I change the work flows?</h2> +<div id="outline-container-orge2aecf8" class="outline-2"> +<h2 id="orge2aecf8"><span class="section-number-2">12</span> How do I change the work flows?</h2> <div class="outline-text-2" id="text-12"> <p> See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>! @@ -456,8 +458,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<div id="outline-container-org2bdd0eb" class="outline-2"> -<h2 id="org2bdd0eb"><span class="section-number-2">13</span> How do I change the source code?</h2> +<div id="outline-container-orgd45b3bc" class="outline-2"> +<h2 id="orgd45b3bc"><span class="section-number-2">13</span> How do I change the source code?</h2> <div class="outline-text-2" id="text-13"> <p> Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, fork/clone the repository, change @@ -467,8 +469,8 @@ many PRs we already merged. </div> </div> -<div id="outline-container-org0468035" class="outline-2"> -<h2 id="org0468035"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2> +<div id="outline-container-org2bb9455" class="outline-2"> +<h2 id="org2bb9455"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2> <div class="outline-text-2" id="text-14"> <p> Restrictive data licenses are hampering data sharing and reproducible @@ -484,8 +486,8 @@ In all honesty: we prefer both data and software to be free. </div> </div> -<div id="outline-container-org246712c" class="outline-2"> -<h2 id="org246712c"><span class="section-number-2">15</span> How do I deal with private data and privacy?</h2> +<div id="outline-container-org62bf23f" class="outline-2"> +<h2 id="org62bf23f"><span class="section-number-2">15</span> How do I deal with private data and privacy?</h2> <div class="outline-text-2" id="text-15"> <p> A public sequence resource is about public data. Metadata can refer to @@ -496,8 +498,8 @@ plan to combine identifiers with clinical data stored securely at </div> </div> -<div id="outline-container-org29eb659" class="outline-2"> -<h2 id="org29eb659"><span class="section-number-2">16</span> How do I communicate with you?</h2> +<div id="outline-container-org40c6da0" class="outline-2"> +<h2 id="org40c6da0"><span class="section-number-2">16</span> How do I communicate with you?</h2> <div class="outline-text-2" id="text-16"> <p> We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link">gitter channel</a> you can join. @@ -505,8 +507,8 @@ We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm </div> </div> -<div id="outline-container-orgce9d1ee" class="outline-2"> -<h2 id="orgce9d1ee"><span class="section-number-2">17</span> Who are the sponsors?</h2> +<div id="outline-container-org1f27c44" class="outline-2"> +<h2 id="org1f27c44"><span class="section-number-2">17</span> Who are the sponsors?</h2> <div class="outline-text-2" id="text-17"> <p> The main sponsors are listed in the footer. In addition to the time @@ -517,7 +519,7 @@ for donating COVID-19 related compute time. </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 2020-05-28 Thu 08:40</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 2020-05-29 Fri 08:26</small>. </div> </body> </html> diff --git a/doc/web/about.org b/doc/web/about.org index 8e535dc..b6387e7 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -63,6 +63,8 @@ public resources, including GISAID. for bulk uploads 3. We provide a live SPARQL end-point for all metadata 2. We provide free data analysis and sequence comparison triggered on data upload +3. We do real work for you, with this [[https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od][link]] you can see the last + run took 5.5 hours! 4. We provide free downloads of all computed output 3. There is no need to set up pipelines and/or compute clusters 4. All workflows get triggered on uploading a new sequence diff --git a/doc/web/download.html b/doc/web/download.html index 493af11..2fde013 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> -<!-- 2020-05-24 Sun 11:29 --> +<!-- 2020-05-29 Fri 08:27 --> <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 +247,44 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org42addaa">1. FASTA files</a></li> -<li><a href="#org04bd8c7">2. Metadata</a></li> -<li><a href="#orgead2f03">3. Pangenome</a> +<li><a href="#orgdde8653">1. Workflow runs</a></li> +<li><a href="#org406920c">2. FASTA files</a></li> +<li><a href="#org8e639a6">3. Metadata</a></li> +<li><a href="#org940e0a9">4. Pangenome</a> <ul> -<li><a href="#org8ea7d40">3.1. Pangenome GFA format</a></li> -<li><a href="#orge7808d6">3.2. Pangenome in ODGI format</a></li> -<li><a href="#orgaadcde8">3.3. Pangenome RDF format</a></li> -<li><a href="#orga3a0408">3.4. Pangenome Browser format</a></li> +<li><a href="#org032f85b">4.1. Pangenome GFA format</a></li> +<li><a href="#org0c3f155">4.2. Pangenome in ODGI format</a></li> +<li><a href="#org08a5353">4.3. Pangenome RDF format</a></li> +<li><a href="#org369f04f">4.4. Pangenome Browser format</a></li> </ul> </li> -<li><a href="#org1bbb7e6">4. Log of workflow output</a></li> -<li><a href="#orgd16b2c8">5. All files</a></li> -<li><a href="#org9d40ed2">6. Planned</a> +<li><a href="#orge6e1f1b">5. Log of workflow output</a></li> +<li><a href="#org90d906c">6. All files</a></li> +<li><a href="#org95b1d68">7. Planned</a> <ul> -<li><a href="#org70cb9d5">6.1. Raw sequence data</a></li> -<li><a href="#org38cfa2e">6.2. Multiple Sequence Alignment (MSA)</a></li> -<li><a href="#org507c7dd">6.3. Phylogenetic tree</a></li> -<li><a href="#orgca26edf">6.4. Protein prediction</a></li> +<li><a href="#org629d3ef">7.1. Raw sequence data</a></li> +<li><a href="#org2f745c7">7.2. Multiple Sequence Alignment (MSA)</a></li> +<li><a href="#org8d3edf7">7.3. Phylogenetic tree</a></li> +<li><a href="#orge0c103c">7.4. Protein prediction</a></li> </ul> </li> </ul> </div> </div> -<div id="outline-container-org42addaa" class="outline-2"> -<h2 id="org42addaa"><span class="section-number-2">1</span> FASTA files</h2> +<div id="outline-container-orgdde8653" class="outline-2"> +<h2 id="orgdde8653"><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/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">here</a>. +</p> +</div> +</div> + +<div id="outline-container-org406920c" class="outline-2"> +<h2 id="org406920c"><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 FASTA files. They can be referred to from metadata individually. We also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup.fasta">FASTA download</a>. @@ -282,9 +292,9 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-org04bd8c7" class="outline-2"> -<h2 id="org04bd8c7"><span class="section-number-2">2</span> Metadata</h2> -<div class="outline-text-2" id="text-2"> +<div id="outline-container-org8e639a6" class="outline-2"> +<h2 id="org8e639a6"><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 @@ -305,18 +315,18 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-orgead2f03" class="outline-2"> -<h2 id="orgead2f03"><span class="section-number-2">3</span> Pangenome</h2> -<div class="outline-text-2" id="text-3"> +<div id="outline-container-org940e0a9" class="outline-2"> +<h2 id="org940e0a9"><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 (VG) provide a succinct encoding of the sequences of many genomes. </p> </div> -<div id="outline-container-org8ea7d40" class="outline-3"> -<h3 id="org8ea7d40"><span class="section-number-3">3.1</span> Pangenome GFA format</h3> -<div class="outline-text-3" id="text-3-1"> +<div id="outline-container-org032f85b" class="outline-3"> +<h3 id="org032f85b"><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 by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. @@ -324,9 +334,9 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<div id="outline-container-orge7808d6" class="outline-3"> -<h3 id="orge7808d6"><span class="section-number-3">3.2</span> Pangenome in ODGI format</h3> -<div class="outline-text-3" id="text-3-2"> +<div id="outline-container-org0c3f155" class="outline-3"> +<h3 id="org0c3f155"><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 implementation. @@ -334,9 +344,9 @@ implementation. </div> </div> -<div id="outline-container-orgaadcde8" class="outline-3"> -<h3 id="orgaadcde8"><span class="section-number-3">3.3</span> Pangenome RDF format</h3> -<div class="outline-text-3" id="text-3-3"> +<div id="outline-container-org08a5353" class="outline-3"> +<h3 id="org08a5353"><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 graph can be downloaded from @@ -346,9 +356,9 @@ graph can be downloaded from </div> -<div id="outline-container-orga3a0408" class="outline-3"> -<h3 id="orga3a0408"><span class="section-number-3">3.4</span> Pangenome Browser format</h3> -<div class="outline-text-3" id="text-3-4"> +<div id="outline-container-org369f04f" class="outline-3"> +<h3 id="org369f04f"><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 <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">results/1/chunk001200.bin1.schematic.json</a> are consumed by the @@ -358,62 +368,62 @@ Pangenome browser. </div> </div> -<div id="outline-container-org1bbb7e6" class="outline-2"> -<h2 id="org1bbb7e6"><span class="section-number-2">4</span> Log of workflow output</h2> -<div class="outline-text-2" id="text-4"> +<div id="outline-container-orge6e1f1b" class="outline-2"> +<h2 id="orge6e1f1b"><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. </p> </div> </div> -<div id="outline-container-orgd16b2c8" class="outline-2"> -<h2 id="orgd16b2c8"><span class="section-number-2">5</span> All files</h2> -<div class="outline-text-2" id="text-5"> +<div id="outline-container-org90d906c" class="outline-2"> +<h2 id="org90d906c"><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> </p> </div> </div> -<div id="outline-container-org9d40ed2" class="outline-2"> -<h2 id="org9d40ed2"><span class="section-number-2">6</span> Planned</h2> -<div class="outline-text-2" id="text-6"> +<div id="outline-container-org95b1d68" class="outline-2"> +<h2 id="org95b1d68"><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-org70cb9d5" class="outline-3"> -<h3 id="org70cb9d5"><span class="section-number-3">6.1</span> Raw sequence data</h3> -<div class="outline-text-3" id="text-6-1"> +<div id="outline-container-org629d3ef" class="outline-3"> +<h3 id="org629d3ef"><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>. </p> </div> </div> -<div id="outline-container-org38cfa2e" class="outline-3"> -<h3 id="org38cfa2e"><span class="section-number-3">6.2</span> Multiple Sequence Alignment (MSA)</h3> -<div class="outline-text-3" id="text-6-2"> +<div id="outline-container-org2f745c7" class="outline-3"> +<h3 id="org2f745c7"><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>. </p> </div> </div> -<div id="outline-container-org507c7dd" class="outline-3"> -<h3 id="org507c7dd"><span class="section-number-3">6.3</span> Phylogenetic tree</h3> -<div class="outline-text-3" id="text-6-3"> +<div id="outline-container-org8d3edf7" class="outline-3"> +<h3 id="org8d3edf7"><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>. </p> </div> </div> -<div id="outline-container-orgca26edf" class="outline-3"> -<h3 id="orgca26edf"><span class="section-number-3">6.4</span> Protein prediction</h3> -<div class="outline-text-3" id="text-6-4"> +<div id="outline-container-orge0c103c" class="outline-3"> +<h3 id="orge0c103c"><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. </p> @@ -422,7 +432,7 @@ We aim to make protein predictions available. </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 2020-05-24 Sun 11:29</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 2020-05-29 Fri 08:27</small>. </div> </body> </html> diff --git a/doc/web/download.org b/doc/web/download.org index 3b4c40a..2781d67 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -2,6 +2,7 @@ #+AUTHOR: Pjotr Prins * Table of Contents :TOC:noexport: + - [[#workflow-runs][Workflow runs]] - [[#fasta-files][FASTA files]] - [[#metadata][Metadata]] - [[#pangenome][Pangenome]] @@ -17,6 +18,10 @@ - [[#phylogenetic-tree][Phylogenetic tree]] - [[#protein-prediction][Protein prediction]] +* Workflow runs + +The last runs can be viewed [[https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od][here]]. + * FASTA files The *public sequence resource* provides all uploaded sequences as |