From 1f470de17eba27d4406bb2840d5301cab3ccffda Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 5 Nov 2020 11:31:50 +0000 Subject: Using 'DOCS' instead of 'BLOG' --- doc/web/download.html | 172 ++++++++++++++++++++++---------------------------- doc/web/download.org | 2 +- 2 files changed, 75 insertions(+), 99 deletions(-) (limited to 'doc') 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"> - + Download @@ -40,7 +40,7 @@ } pre.src { position: relative; - overflow: visible; + overflow: auto; padding-top: 1.2em; } pre.src:before { @@ -194,50 +194,26 @@ /*]]>*/--> @@ -247,35 +223,35 @@ for the JavaScript code in this tag.

Table of Contents

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-

1 Workflow runs

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+

1 Workflow runs

The last runs can be viewed here. If you click on a run you can see @@ -286,8 +262,8 @@ is listed under Data collections. All current data is listed

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-

2 FASTA files

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+

2 FASTA files

The public sequence resource provides all uploaded sequences as @@ -297,15 +273,15 @@ also provide a single file -

3 Metadata

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+

3 Metadata

Metadata can be downloaded as Turtle RDF as a mergedmetadat.ttl which 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 BLOG. +the DOCS

@@ -320,8 +296,8 @@ graph can be downloaded from below Pangenome RDF format.

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4 Pangenome

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+

4 Pangenome

Pangenome data is made available in multiple guises. Variation graphs @@ -329,8 +305,8 @@ Pangenome data is made available in multiple guises. Variation graphs

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4.1 Pangenome GFA format

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4.1 Pangenome GFA format

GFA is a standard for graphical fragment assembly and consumed @@ -339,8 +315,8 @@ by tools such as vgtools.

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4.2 Pangenome in ODGI format

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+

4.2 Pangenome in ODGI format

ODGI is a format that supports an optimised dynamic genome/graph @@ -349,8 +325,8 @@ implementation.

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4.3 Pangenome RDF format

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4.3 Pangenome RDF format

An RDF file that includes the sequences themselves in a variation @@ -361,8 +337,8 @@ graph can be downloaded from

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4.4 Pangenome Browser format

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4.4 Pangenome Browser format

The many JSON files that are named as @@ -373,8 +349,8 @@ Pangenome browser.

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5 Log of workflow output

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5 Log of workflow output

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.

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6 All files

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+

6 All files

https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/ @@ -391,16 +367,16 @@ Including in below link is a log file of the last workflow runs.

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7 Planned

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7 Planned

We are planning the add the following output (see also

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7.1 Raw sequence data

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7.1 Raw sequence data

See fastq tracker and BAM tracker. @@ -408,8 +384,8 @@ See fastq track

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7.2 Multiple Sequence Alignment (MSA)

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7.3 Phylogenetic tree

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7.4 Protein prediction

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7.4 Protein prediction

We aim to make protein predictions available. @@ -436,8 +412,8 @@ We aim to make protein predictions available.

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8 Source code

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8 Source code

All source code for this website and tooling is available @@ -447,8 +423,8 @@ from

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9 Citing PubSeq

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9 Citing PubSeq

See the FAQ. @@ -457,7 +433,7 @@ See the FAQ.

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Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-24 Mon 03:07. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-11-05 Thu 05:26.
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]]. -- cgit v1.2.3