From 9fb2d889105753b52ba6380f7f1e6f8732daefe2 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 12 Jun 2020 04:58:15 -0500 Subject: Added github repo to Download --- doc/web/download.html | 106 ++++++++++++++++++++++++++++---------------------- doc/web/download.org | 7 ++++ 2 files changed, 66 insertions(+), 47 deletions(-) (limited to 'doc/web') 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"> - + Download @@ -247,33 +247,34 @@ 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 @@ -284,8 +285,8 @@ 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 @@ -295,8 +296,8 @@ 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 @@ -318,8 +319,8 @@ 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 @@ -327,8 +328,8 @@ 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 @@ -337,8 +338,8 @@ 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 @@ -347,8 +348,8 @@ 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 @@ -359,8 +360,8 @@ 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 @@ -371,8 +372,8 @@ 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. @@ -380,8 +381,8 @@ 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/ @@ -389,16 +390,16 @@ 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. @@ -406,8 +407,8 @@ See fastq track

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7.2 Multiple Sequence Alignment (MSA)

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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 2020-05-30 Sat 10:40. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-06-12 Fri 04:41.
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 -- cgit v1.2.3