From e5be5fe049bb0319fedb65248cb562369735d879 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 24 May 2020 11:33:07 -0500 Subject: Colors and protein prediction --- bh20simplewebuploader/templates/org-header.html | 2 +- doc/web/download.html | 113 +++++++++++++++++------- doc/web/download.org | 5 ++ 3 files changed, 89 insertions(+), 31 deletions(-) diff --git a/bh20simplewebuploader/templates/org-header.html b/bh20simplewebuploader/templates/org-header.html index fdf9e14..b0e60c8 100644 --- a/bh20simplewebuploader/templates/org-header.html +++ b/bh20simplewebuploader/templates/org-header.html @@ -222,7 +222,7 @@ div[id="text-table-of-contents"]{ border-width: 1px; } div[class^="outline-text"] { - background-color:#ebe6f0; + background-color:white; border-style: dotted; border-color: #98bf21; border-width: 1px; diff --git a/doc/web/download.html b/doc/web/download.html index 879e8d4..493af11 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 @@ -247,24 +247,32 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 FASTA files

+
+

1 FASTA files

The public sequence resource provides all uploaded sequences as @@ -274,8 +282,8 @@ also provide a single file -

2 Metadata

+
+

2 Metadata

Metadata can be downloaded as Turtle RDF as a mergedmetadat.ttl which @@ -297,8 +305,8 @@ graph can be downloaded from below Pangenome RDF format.

-
-

3 Pangenome

+
+

3 Pangenome

Pangenome data is made available in multiple guises. Variation graphs @@ -306,8 +314,8 @@ Pangenome data is made available in multiple guises. Variation graphs

-
-

3.1 Pangenome GFA format

+
+

3.1 Pangenome GFA format

GFA is a standard for graphical fragment assembly and consumed @@ -316,18 +324,18 @@ by tools such as vgtools.

-
-

3.2 Pangenome in ODGI format

+
+

3.2 Pangenome in ODGI format

-ODGI is a format that supports an optimized dynamic genome/graph +ODGI is a format that supports an optimised dynamic genome/graph implementation.

-
-

3.3 Pangenome RDF format

+
+

3.3 Pangenome RDF format

An RDF file that includes the sequences themselves in a variation @@ -338,8 +346,8 @@ graph can be downloaded from

-
-

3.4 Pangenome Browser format

+
+

3.4 Pangenome Browser format

The many JSON files that are named as @@ -350,8 +358,8 @@ Pangenome browser.

-
-

4 Log of workflow output

+
+

4 Log of workflow output

Including in below link is a log file of the last workflow runs. @@ -359,17 +367,62 @@ Including in below link is a log file of the last workflow runs.

-
-

5 All files

+ + +
+

6 Planned

+
+

+We are planning the add the following output (see also +

+
+ +
+

6.1 Raw sequence data

+
+

+See fastq tracker and BAM tracker. +

+
+
+ +
+

6.2 Multiple Sequence Alignment (MSA)

+
+

+See MSA tracker. +

+
+
+ +
+

6.3 Phylogenetic tree

+
+

+See Phylo tracker. +

+
+
+ +
+

6.4 Protein prediction

+
+

+We aim to make protein predictions available. +

+
+
+
-
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-24 Sun 11:11. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-24 Sun 11:29.
diff --git a/doc/web/download.org b/doc/web/download.org index c48b6d8..3b4c40a 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -15,6 +15,7 @@ - [[#raw-sequence-data][Raw sequence data]] - [[#multiple-sequence-alignment-msa][Multiple Sequence Alignment (MSA)]] - [[#phylogenetic-tree][Phylogenetic tree]] + - [[#protein-prediction][Protein prediction]] * FASTA files @@ -87,3 +88,7 @@ See [[https://github.com/arvados/bh20-seq-resource/issues/11][MSA tracker]]. ** Phylogenetic tree See [[https://github.com/arvados/bh20-seq-resource/issues/43][Phylo tracker]]. + +** Protein prediction + +We aim to make protein predictions available. -- cgit v1.2.3