From 8e052cb7355eed7ce4d7075b23c9b0439285f84e Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Sun, 26 Jul 2020 18:02:41 +0200 Subject: updated org files, removing unuseful information and adding the BCC2020 video talk and poster links in the about page --- doc/blog/using-covid-19-pubseq-part2.html | 33 +++---------------------------- doc/blog/using-covid-19-pubseq-part2.org | 25 +---------------------- doc/blog/using-covid-19-pubseq-part3.html | 2 +- doc/blog/using-covid-19-pubseq-part3.org | 2 +- 4 files changed, 6 insertions(+), 56 deletions(-) (limited to 'doc/blog') diff --git a/doc/blog/using-covid-19-pubseq-part2.html b/doc/blog/using-covid-19-pubseq-part2.html index c047441..c041ebe 100644 --- a/doc/blog/using-covid-19-pubseq-part2.html +++ b/doc/blog/using-covid-19-pubseq-part2.html @@ -259,39 +259,12 @@ for the JavaScript code in this tag. -

-As part of the COVID-19 Biohackathon 2020 we formed a working group to -create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for -Corona virus sequences. The general idea is to create a repository -that has a low barrier to entry for uploading sequence data using best -practices. I.e., data published with a creative commons 4.0 (CC-4.0) -license with metadata using state-of-the art standards and, perhaps -most importantly, providing standardised workflows that get triggered -on upload, so that results are immediately available in standardised -data formats. -

1 Finding output of workflows

-

-As part of the COVID-19 Biohackathon 2020 we formed a working group to -create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for -Corona virus sequences. The general idea is to create a repository -that has a low barrier to entry for uploading sequence data using best -practices. I.e., data published with a creative commons 4.0 (CC-4.0) -license with metadata using state-of-the art standards and, perhaps -most importantly, providing standardised workflows that get triggered -on upload, so that results are immediately available in standardised -data formats. -

-
-
-
-

2 Introduction

-
-

+

We are using Arvados to run common workflow language (CWL) pipelines. The most recent output is on display on a web page (with time stamp) and a full list is generated here. It is nice to start up, but for @@ -302,7 +275,7 @@ want to wade through thousands of output files!

-

3 The Arvados file interface

+

2 The Arvados file interface

Arvados has the web server, but it also has a REST API and associated @@ -384,7 +357,7 @@ arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839d

-

4 Using the Arvados API

+

3 TODO Using the Arvados API

diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org index d2a1cbc..349fd06 100644 --- a/doc/blog/using-covid-19-pubseq-part2.org +++ b/doc/blog/using-covid-19-pubseq-part2.org @@ -8,36 +8,13 @@ #+HTML_LINK_HOME: http://covid19.genenetwork.org #+HTML_HEAD: -As part of the COVID-19 Biohackathon 2020 we formed a working group to -create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for -Corona virus sequences. The general idea is to create a repository -that has a low barrier to entry for uploading sequence data using best -practices. I.e., data published with a creative commons 4.0 (CC-4.0) -license with metadata using state-of-the art standards and, perhaps -most importantly, providing standardised workflows that get triggered -on upload, so that results are immediately available in standardised -data formats. - * Table of Contents :TOC:noexport: - [[#finding-output-of-workflows][Finding output of workflows]] - - [[#introduction][Introduction]] - [[#the-arvados-file-interface][The Arvados file interface]] - [[#using-the-arvados-api][Using the Arvados API]] * Finding output of workflows -As part of the COVID-19 Biohackathon 2020 we formed a working group to -create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for -Corona virus sequences. The general idea is to create a repository -that has a low barrier to entry for uploading sequence data using best -practices. I.e., data published with a creative commons 4.0 (CC-4.0) -license with metadata using state-of-the art standards and, perhaps -most importantly, providing standardised workflows that get triggered -on upload, so that results are immediately available in standardised -data formats. - -* Introduction - We are using Arvados to run common workflow language (CWL) pipelines. The most recent output is on display on a [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][web page]] (with time stamp) and a full list is generated [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. It is nice to start up, but for @@ -81,4 +58,4 @@ its listed UUID: : arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839de18290843a@5ed7f3c5 -* Using the Arvados API +* TODO Using the Arvados API diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html index 91879b0..df4a286 100644 --- a/doc/blog/using-covid-19-pubseq-part3.html +++ b/doc/blog/using-covid-19-pubseq-part3.html @@ -625,7 +625,7 @@ The web interface using this exact same script so it should just work

6.2 Example: uploading bulk GenBank sequences

-We also use above script to bulk upload GenBank sequences with a FASTA +We also use above script to bulk upload GenBank sequences with a FASTA and YAML extractor specific for GenBank. This means that the steps we took above for uploading a GenBank sequence are already automated.

diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index 03f37ab..e8fee36 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -234,6 +234,6 @@ The web interface using this exact same script so it should just work ** Example: uploading bulk GenBank sequences -We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/from_genbank_to_fasta_and_yaml.py][FASTA +We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA and YAML]] extractor specific for GenBank. This means that the steps we took above for uploading a GenBank sequence are already automated. -- cgit v1.2.3