From 87f3fb187ea7a956a3bd2fe224a3ea06ff1d760b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 17 Jul 2020 11:42:15 +0100 Subject: Started EBI submission --- doc/blog/using-covid-19-pubseq-part6.org | 11 +++++++---- scripts/submit_ebi/example/project-submission.xml | 11 +++++++++++ scripts/submit_ebi/example/project.xml | 9 +++++++++ 3 files changed, 27 insertions(+), 4 deletions(-) create mode 100644 scripts/submit_ebi/example/project-submission.xml create mode 100644 scripts/submit_ebi/example/project.xml diff --git a/doc/blog/using-covid-19-pubseq-part6.org b/doc/blog/using-covid-19-pubseq-part6.org index 2a7c593..2d1c5e0 100644 --- a/doc/blog/using-covid-19-pubseq-part6.org +++ b/doc/blog/using-covid-19-pubseq-part6.org @@ -23,7 +23,10 @@ why not export the same to EBI too with the least amount of effort? COVID-19 PubSeq is a data source - both sequence data and metadata - that can be used to push data to other sources, such as EBI. You can -register [[https://ena-docs.readthedocs.io/en/latest/submit/samples/programmatic.html][samples programmatically]] with a specific XML interface. +register [[https://ena-docs.readthedocs.io/en/latest/submit/samples/programmatic.html][samples programmatically]] with a specific XML interface. Note +that (at this point) if you want to submit a sequence (FASTA) it can +only be done through the [[https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html][Webin-CLI]]. Raw data (FASTQ) can go through +the XML interface. EBI sequence resources are presented through ENA. For example [[https://www.ebi.ac.uk/ena/browser/view/MT394864][Sequence: MT394864.1]]. @@ -42,9 +45,9 @@ EBI has XML Formats for - PROJECT with the schemas listed [[ftp://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/][here]]. Since we are submitting sequences we -should follow submitting [[https://ena-docs.readthedocs.io/en/latest/submit/assembly.html][full genome assembly guidelines]] and [[https://ena-docs.readthedocs.io/en/latest/submit/general-guide/programmatic.html][ENA -guidelines]]. The first step is to define the study, next the sample and -finally the sequence (assembly). +should follow submitting [[https://ena-docs.readthedocs.io/en/latest/submit/assembly.html][full genome assembly guidelines]] and +[[https://ena-docs.readthedocs.io/en/latest/submit/general-guide/programmatic.html][ENA guidelines]]. The first step is to define the study, next the sample +and finally the sequence (assembly). * Defining the EBI study diff --git a/scripts/submit_ebi/example/project-submission.xml b/scripts/submit_ebi/example/project-submission.xml new file mode 100644 index 0000000..2d3ddc1 --- /dev/null +++ b/scripts/submit_ebi/example/project-submission.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + diff --git a/scripts/submit_ebi/example/project.xml b/scripts/submit_ebi/example/project.xml new file mode 100644 index 0000000..90704ab --- /dev/null +++ b/scripts/submit_ebi/example/project.xml @@ -0,0 +1,9 @@ + + + Testing PubSeq Sample uploads + This study aimed to allow for uploading sequences from PubSeq + + + + + -- cgit v1.2.3