Commit 9c706ab1 authored by Aaron Petkau's avatar Aaron Petkau

Added readme

parent 309f7372
# IRIDA API Scripts
A collection of scripts for interacting with the IRIDA API to extract information.
# Scripts
## `irida-coverage-report.pl`
Exports the estimated coverage for each sample in the given IRIDA Project(s) to an excel spreadsheet.
### Usage
```bash
Usage:
irida-coverage-report.pl [--help] --username USERNAME --project-id [PROJECT_ID] --reference-size [REFERENCE_SIZE] [--password PASSWORD] [--api-url URL] [--client-id CLIENT_ID] [--client-secret CLIENT_SECRET] [--report FILENAME]
--help Print this message
--username Your IRIDA/NGS Archive username
--password Your IRIDA/NGS Archive password (if you do not provide a value, you will be prompted to enter one)
--api-url The IRIDA API that you want to connect to (default: NML IRIDA)
--client-id The Client ID you were issued (default: NML IRIDA)
--client-secret The Client secret you were issued (default: NML IRIDA)
--project-id The particular project ID to check (can specify more than one).
--reference-size The reference genome size (in bp).
--report The filename you'd like to use for writing out the report (default: irida-report.xlsx)
Example:
irida-coverage-report.pl --username user --reference-size 4000000 --project-id 1
Exports coverage values for the project with identifier 1 to the default file "irida-report.xlsx", calculating minimum coverage using a reference genome size of 4,000,000 bp.
irida-coverage-report.pl --username user --reference-size 3500000 --project-id 3 --project-id 4 --report my-report.xlsx
Exports coverage values for the projects 3 and 4 to the file "my-report.xlsx", calculating minimum coverage using a reference genome size of 3,500,000 bp.
```
### Output
A spreadsheet listing the estimated coverage for each sample in the project(s).
![coverage-output](docs/images/coverage-output.png)
### Dependencies
* Perl
* Perl Modules
* `Excel::Writer::XLSX` - Install with `cpanm Excel::Writer::XLSX`
# Legal
Copyright 2018 Government of Canada
Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this work except in compliance with the License. You may obtain a copy of the
License at:
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed
under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
CONDITIONS OF ANY KIND, either express or implied. See the License for the
specific language governing permissions and limitations under the License.
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