Repository ncbi_eutils_efetch

Name: ncbi_eutils_efetch

Owner: iuc

Synopsis: Wrapper for NCBI application NCBI EFetch

Detailed description:

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>

Content homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils

Link to this repository: https://toolshed.g2.bx.psu.edu/view/iuc/ncbi_eutils_efetch/0ccb2855dd55

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch

Type: unrestricted

Revision: 10:0ccb2855dd55

This revision can be installed: True

Times cloned / installed: 982

Repository README files - may contain important installation or license information

Readme files

Galaxy NCBI Entrez Tools

This repo requires a readme as 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 jobs_conf.xml snippet 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>