diff options
Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part3.org')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 22 |
1 files changed, 20 insertions, 2 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index abc260c..fb68251 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -228,7 +228,25 @@ command line : python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml after installing dependencies (also described in [[https://github.com/arvados/bh20-seq-resource/blob/master/doc/INSTALL.md][INSTALL]] with the GNU -Guix package manager). +Guix package manager). The ~--help~ shows + +#+begin_src sh +Entering sequence uploader +usage: main.py [-h] [--validate] [--skip-qc] [--trusted] metadata sequence_p1 [sequence_p2] + +Upload SARS-CoV-19 sequences for analysis + +positional arguments: + metadata sequence metadata json + sequence_p1 sequence FASTA/FASTQ + sequence_p2 sequence FASTQ pair + +optional arguments: + -h, --help show this help message and exit + --validate Dry run, validate only + --skip-qc Skip local qc check + --trusted Trust local validation and add directly to validated project +#+end_src The web interface using this exact same script so it should just work (TM). @@ -265,4 +283,4 @@ and execute 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 +You will find the YAML files in the `yaml` folder which will be created in the same directory. |