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Diffstat (limited to 'doc/web')
| -rw-r--r-- | doc/web/download.html | 99 | ||||
| -rw-r--r-- | doc/web/download.org | 5 |
2 files changed, 55 insertions, 49 deletions
diff --git a/doc/web/download.html b/doc/web/download.html index 2fde013..001b071 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> -<!-- 2020-05-29 Fri 08:27 --> +<!-- 2020-05-30 Sat 10:40 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Download</title> @@ -247,42 +247,45 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<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> +<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> <ul> -<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> +<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> </ul> </li> -<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> +<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> <ul> -<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> +<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> </ul> </li> </ul> </div> </div> -<div id="outline-container-orgdde8653" class="outline-2"> -<h2 id="orgdde8653"><span class="section-number-2">1</span> Workflow runs</h2> +<div id="outline-container-orgcde4e6b" class="outline-2"> +<h2 id="orgcde4e6b"><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>. +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 +the workflows that ran under <code>Processes</code>. Output (also intermediate) +is listed under <code>Data collections</code>. All current data is listed +<a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>. Note that it takes time for a run to complete and show. </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 id="outline-container-org1b46d7e" class="outline-2"> +<h2 id="org1b46d7e"><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 @@ -292,8 +295,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-org8e639a6" class="outline-2"> -<h2 id="org8e639a6"><span class="section-number-2">3</span> Metadata</h2> +<div id="outline-container-orgf2db570" class="outline-2"> +<h2 id="orgf2db570"><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 @@ -315,8 +318,8 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-org940e0a9" class="outline-2"> -<h2 id="org940e0a9"><span class="section-number-2">4</span> Pangenome</h2> +<div id="outline-container-org9f89b24" class="outline-2"> +<h2 id="org9f89b24"><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 @@ -324,8 +327,8 @@ Pangenome data is made available in multiple guises. Variation graphs </p> </div> -<div id="outline-container-org032f85b" class="outline-3"> -<h3 id="org032f85b"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> +<div id="outline-container-org436ee36" class="outline-3"> +<h3 id="org436ee36"><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 @@ -334,8 +337,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<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 id="outline-container-org6cd667b" class="outline-3"> +<h3 id="org6cd667b"><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 @@ -344,8 +347,8 @@ implementation. </div> </div> -<div id="outline-container-org08a5353" class="outline-3"> -<h3 id="org08a5353"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> +<div id="outline-container-org220b6cb" class="outline-3"> +<h3 id="org220b6cb"><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 @@ -356,8 +359,8 @@ graph can be downloaded from </div> -<div id="outline-container-org369f04f" class="outline-3"> -<h3 id="org369f04f"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> +<div id="outline-container-org78f267a" class="outline-3"> +<h3 id="org78f267a"><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 @@ -368,8 +371,8 @@ Pangenome browser. </div> </div> -<div id="outline-container-orge6e1f1b" class="outline-2"> -<h2 id="orge6e1f1b"><span class="section-number-2">5</span> Log of workflow output</h2> +<div id="outline-container-org8cced34" class="outline-2"> +<h2 id="org8cced34"><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. @@ -377,8 +380,8 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org90d906c" class="outline-2"> -<h2 id="org90d906c"><span class="section-number-2">6</span> All files</h2> +<div id="outline-container-org9d23c51" class="outline-2"> +<h2 id="org9d23c51"><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> @@ -386,16 +389,16 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org95b1d68" class="outline-2"> -<h2 id="org95b1d68"><span class="section-number-2">7</span> Planned</h2> +<div id="outline-container-org105d2d4" class="outline-2"> +<h2 id="org105d2d4"><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-org629d3ef" class="outline-3"> -<h3 id="org629d3ef"><span class="section-number-3">7.1</span> Raw sequence data</h3> +<div id="outline-container-org52bb570" class="outline-3"> +<h3 id="org52bb570"><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>. @@ -403,8 +406,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track </div> </div> -<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 id="outline-container-org68c178c" class="outline-3"> +<h3 id="org68c178c"><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>. @@ -412,8 +415,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker </div> </div> -<div id="outline-container-org8d3edf7" class="outline-3"> -<h3 id="org8d3edf7"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> +<div id="outline-container-org9ccf15c" class="outline-3"> +<h3 id="org9ccf15c"><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>. @@ -421,8 +424,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track </div> </div> -<div id="outline-container-orge0c103c" class="outline-3"> -<h3 id="orge0c103c"><span class="section-number-3">7.4</span> Protein prediction</h3> +<div id="outline-container-org31c2b68" class="outline-3"> +<h3 id="org31c2b68"><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. @@ -432,7 +435,7 @@ 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 2020-05-29 Fri 08:27</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 2020-05-30 Sat 10:40</small>. </div> </body> </html> diff --git a/doc/web/download.org b/doc/web/download.org index 2781d67..da6a9a7 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -20,7 +20,10 @@ * Workflow runs -The last runs can be viewed [[https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od][here]]. +The last runs can be viewed [[https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects][here]]. If you click on a run you can see +the workflows that ran under ~Processes~. Output (also intermediate) +is listed under ~Data collections~. All current data is listed +[[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. Note that it takes time for a run to complete and show. * FASTA files |