From 503fe6e31cc679422c2ce082942e4d938fc90ffd Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 25 Jun 2020 16:26:29 +0200 Subject: [PATCH] Documentation update --- README.md | 72 ++++++++++++++++++++++++++++++++++++++++--------------- 1 file changed, 53 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 33b98bc..d46c27b 100644 --- a/README.md +++ b/README.md @@ -16,20 +16,13 @@ The program to perform the following actions: * cancel: cancel a private object and its dependent objects (**under development**) * release: release a private object immediately to the public (**under development**) -## The tool dependencies in LINUX +## Tool dependencies * curl -* Genshi -* subprocess -* shlex -* json -* argparse -* hashlib -* ftplib -* uuid -* datetime -* lxml -* pandas +* python 2.7+ including following packages: + * Genshi + * lxml + * pandas ## Installation @@ -37,16 +30,53 @@ The program to perform the following actions: pip install ena-upload-cli ``` +> Be aware that Windows can give problems with the `curl` commands executed by the script. Check that curl is available in your PATH. + ## Usage + ``` -ENA_upload [-h] --action {add,modify} [--study STUDY] - --center CENTER_NAME --webin_id - WEBIN_ID --password PASSWORD +usage: ENA_upload [-h] --action {add,modify,cancel,release} [--study STUDY] [--sample SAMPLE] [--experiment EXPERIMENT] [--run RUN] - [--data [FILE [FILE ...]]] + [--data [FILE [FILE ...]]] --center CENTER_NAME --webin_id + WEBIN_ID (--password PASSWORD | --secret SECRET) [-d] + + +optional arguments: + -h, --help show this help message and exit + --action {add,modify,cancel,release} + add: add an object to the archive + modify: modify an object in the + --study STUDY table of STUDY object + --sample SAMPLE table of SAMPLE object + --experiment EXPERIMENT + table of EXPERIMENT object + --run RUN table of RUN object + --data [FILE [FILE ...]] + data for submission + --center CENTER_NAME specific to your Webin account + --webin_id WEBIN_ID the usermane of your Webin account + --password PASSWORD the password of your Webin account + --secret SECRET .secret file containing the password of your Webin account + -d, --dev Flag to use the dev/sandbox endpoint of ENA. ``` -Mandatory arguments: --action, --center, --webin_id, --password. +Mandatory arguments: --action, --center, --webin_id, --password or --secret. + +### ENA Webin + +A Webin can be made [here](https://www.ebi.ac.uk/ena/submit/sra/#home) if you don't have one already. The *--webin_id* parameter makes use of the full username looking like: `Webin-XXXXX`. Visit [Webin online](https://www.ebi.ac.uk/ena/submit/webin) to check on your submissions or [dev Webin](https://wwwdev.ebi.ac.uk/ena/submit/webin) to check on test submissions. + +### The password parameter + +To avoid exposing you password through the terminal history, it is recommended to make use of a `.secret` file, containing your password on the first line. Use instead of the *--password* parameter in the ena-upload-cli tool the *--secret* parameter to specify the location of the .secret file. + + +### dev instance + + +By default the submission will be done using following url to ENA: https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA + +Use the *--dev* flag if you want to do a test submission using the tool by the sandbox dev instance of ENA: https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA. A TEST submission will be discarded within 24 hours ## Test the tool @@ -69,8 +99,12 @@ outputs: test command: **add metadata and sequence data** - `python ena_upload.py --action add --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz` + `ena_upload --action add --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev` test command: **modify a metadata** - `python ena_upload.py --action modify --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies-2020-05-01T14\:21.tsv` + `ena_upload --action modify --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies-2020-05-01T1421.tsv --dev` + +test command **.secret file** + +`ena-upload-cli --action add --center "VIB - UGENT" --webin_id Webin-56059 --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --secret .secret` \ No newline at end of file