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| author | Pjotr Prins | 2020-07-17 11:42:15 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2020-07-17 12:08:43 +0100 |
| commit | 4f3469e2d5395526c0376688ded4340a4834677d (patch) | |
| tree | b55ff07de6bfb6c615c9b640bb4444e7297cd7e7 | |
| parent | 8cf4fee8900e7b146f768791fb7909b334737297 (diff) | |
| download | bh20-seq-resource-4f3469e2d5395526c0376688ded4340a4834677d.tar.gz bh20-seq-resource-4f3469e2d5395526c0376688ded4340a4834677d.tar.lz bh20-seq-resource-4f3469e2d5395526c0376688ded4340a4834677d.zip | |
Started EBI submission
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part6.org | 11 | ||||
| -rw-r--r-- | scripts/submit_ebi/example/project-submission.xml | 11 | ||||
| -rw-r--r-- | scripts/submit_ebi/example/project.xml | 9 |
3 files changed, 27 insertions, 4 deletions
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 @@ +<SUBMISSION> + <ACTIONS> + <ACTION> + <ADD/> + </ACTION> + <ACTION> + <HOLD HoldUntilDate="2020-10-10"/> + </ACTION> + </ACTIONS> +</SUBMISSION> + 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 @@ +<PROJECT_SET> + <PROJECT alias="PubSeq01"> + <TITLE>Testing PubSeq Sample uploads</TITLE> + <DESCRIPTION>This study aimed to allow for uploading sequences from PubSeq</DESCRIPTION> + <SUBMISSION_PROJECT> + <SEQUENCING_PROJECT/> + </SUBMISSION_PROJECT> + </PROJECT> +</PROJECT_SET> |