diff options
Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part3.org')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 16 |
1 files changed, 16 insertions, 0 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index 4d70e7c..abc260c 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -21,6 +21,7 @@ - [[#bulk-sequence-uploader][Bulk sequence uploader]] - [[#run-the-uploader-cli][Run the uploader (CLI)]] - [[#example-uploading-bulk-genbank-sequences][Example: uploading bulk GenBank sequences]] + - [[#example-preparing-metadata][Example: preparing metadata]] * Uploading Data @@ -232,6 +233,7 @@ Guix package manager). The web interface using this exact same script so it should just work (TM). + ** 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/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA @@ -250,3 +252,17 @@ ls $dir_fasta_and_yaml/*.yaml | while read path_code_yaml; do bh20-seq-uploader --skip-qc $path_code_yaml $path_code_fasta done #+END_SRC + + +** Example: preparing metadata + +Usually, metadata are available in tabular format, like spreadsheets. As an example, we provide a script +[[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/esr_samples][esr_samples.py]] to show you how to parse +your metadata in YAML files ready for the upload. To execute the script, go in the ~bh20-seq-resource/scripts/esr_samples +and execute + +#+BEGIN_SRC sh +python3 esr_samples.py +#+END_SRC + +You will find the YAML files in the `yaml` folder which will be created in the same directory.
\ No newline at end of file |