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Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part6.org')
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diff --git a/doc/blog/using-covid-19-pubseq-part6.org b/doc/blog/using-covid-19-pubseq-part6.org index 8964700..6ee68bb 100644 --- a/doc/blog/using-covid-19-pubseq-part6.org +++ b/doc/blog/using-covid-19-pubseq-part6.org @@ -9,11 +9,26 @@ * Table of Contents :TOC:noexport: + - [[#short-version][Short version]] - [[#generating-output-for-ebi][Generating output for EBI]] - [[#defining-the-ebi-study][Defining the EBI study]] - [[#define-the-ebi-sample][Define the EBI sample]] - [[#define-the-ebi-sequence][Define the EBI sequence]] +* Short version + +PubSeq can export files that can be uploaded to EBI/ENA. This saves +you work. Steps are: + +1. Register and account for EBI/ENA as explained [[https://ena-docs.readthedocs.io/en/latest/submit/general-guide.html][here]]. +2. Register a study online or use XML files discussed below +3. Export a sample XML and push to EBI/ENA +4. Zip sequence data and push to EBI/ENA + +Because PubSeq's metadata for is richer than the metadata EBI/ENA asks +for, it is easy to generate and export the forms using the [[http://covid19.genenetwork.org/export][EXPORT]] +page. + * Generating output for EBI Would it not be great an uploader to PubSeq also can export samples @@ -81,6 +96,8 @@ also a submission 'command' is required looking like #+END_SRC +Working XML examples we tested can be found [[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/submit_ebi/example][here]]. + The webin system accepts such sources using a command like : curl -u username:password -F "SUBMISSION=@submission.xml" \ @@ -88,7 +105,7 @@ The webin system accepts such sources using a command like as described [[https://ena-docs.readthedocs.io/en/latest/submit/study/programmatic.html#submit-the-xmls-using-curl][here]]. Note that this is the test server. For the final version use www.ebi.ac.uk instead of wwwdev.ebi.ac.uk. You may also -need the --insecure switch to circumvent certificate checking. +need the =--insecure= switch to circumvent certificate checking. /work in progress (WIP)/ |