Difference between revisions of "EDirect"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|edirect}} |{{#vardefine:url|https://www.ncbi.nlm.nih.gov/books/NBK179288/}} <!--CO...") |
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| − | [[Category:Software]][[Category:Biology]] | + | [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|edirect}} | |{{#vardefine:app|edirect}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | To be able to make many requests to NCBI api you need to have an api key. Log into your ncbi account and copy the text of the api key generated in [https://www.ncbi.nlm.nih.gov/account/settings/ https://www.ncbi.nlm.nih.gov/account/settings/] into ~/.ncbi/api_key file on HiPerGator to be able to exceed the NCBI free request limit. See [https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/] for reference on getting a key. | |
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|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Latest revision as of 14:55, 15 August 2022
Description
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
Environment Modules
Run module spider edirect to find out what environment modules are available for this application.
System Variables
- HPC_EDIRECT_DIR - installation directory
Additional Information
To be able to make many requests to NCBI api you need to have an api key. Log into your ncbi account and copy the text of the api key generated in https://www.ncbi.nlm.nih.gov/account/settings/ into ~/.ncbi/api_key file on HiPerGator to be able to exceed the NCBI free request limit. See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ for reference on getting a key.