aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorPjotr Prins2020-07-17 11:42:15 +0100
committerPjotr Prins2020-07-17 11:42:15 +0100
commit87f3fb187ea7a956a3bd2fe224a3ea06ff1d760b (patch)
treeb55ff07de6bfb6c615c9b640bb4444e7297cd7e7
parent16bb5df907c79cd0ce6bea0015821a2ce51fb992 (diff)
downloadbh20-seq-resource-87f3fb187ea7a956a3bd2fe224a3ea06ff1d760b.tar.gz
bh20-seq-resource-87f3fb187ea7a956a3bd2fe224a3ea06ff1d760b.tar.lz
bh20-seq-resource-87f3fb187ea7a956a3bd2fe224a3ea06ff1d760b.zip
Started EBI submission
-rw-r--r--doc/blog/using-covid-19-pubseq-part6.org11
-rw-r--r--scripts/submit_ebi/example/project-submission.xml11
-rw-r--r--scripts/submit_ebi/example/project.xml9
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>