| Entrez E-Utils provide an interface to the NCBI databases to allow querying and downloading datasets from NCBI This repo requires that administrators should very aware of some restrictions NCBI places on the use of the Entrez service. NCBI requests that you please limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays. This is not a request that the Galaxy tool can easily service, so we've included it in the disclaimer on every tool quite prominently. Failure to comply with NCBI's policies may result in an block until you/the user contacts NCBI and registers the tool ID and their email. Note that these are *IP* level blocks so the Galaxy tools uses a concatenation of the administrator's emails, and the user email, in hopes that NCBI will contact all relevant parties should their system be abused. Additionally, since these are IP level blocks, the Galaxy tool author (@erasche) recommends using the following snippet in config/jobs_conf.xml in order to place a system-wide restriction of 1 concurrent Entrez job amongst all users:: <destination id="entrez" runner="local"> </destination> <limit type="concurrent_jobs" id="entrez">1</limit> <tools> <tool id="ncbi.eutils.efetch" destination="entrez" /> <tool id="ncbi.eutils.esearch" destination="entrez" /> <tool id="ncbi.eutils.epost" destination="entrez" /> <tool id="ncbi.eutils.elink" destination="entrez" /> <tool id="ncbi.eutils.einfo" destination="entrez" /> <tool id="ncbi.eutils.esummary" destination="entrez" /> </tools> |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch
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| Name | Version | Type | |
|---|---|---|---|
| biopython | 1.66 | package | |
| NCBI_EUTILS_CONTACT | set_environment | ||
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| fetch records from NCBI | 1.1 | any | |