Mercurial > repos > iuc > ncbi_eutils_efetch

annotate README.rst @ 3:c09fcbe4b16a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:48:53 +0000
parents 71bcf87a7031
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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1 Galaxy NCBI Entrez Tools
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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2 ========================
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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4 This repo requires a readme as administrators should very aware of some
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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5 restrictions NCBI places on the use of the Entrez service.
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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7 NCBI requests that you please limit large jobs to either weekends or
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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8 between 9:00 PM and 5:00 AM Eastern time during weekdays. This is not a
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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9 request that the Galaxy tool can easily service, so we've included it in
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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10 the disclaimer on every tool quite prominently.
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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12 Failure to comply with NCBI's policies may result in an block until
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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13 you/the user contacts NCBI and registers the tool ID and their email.
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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15 Note that these are *IP* level blocks so the Galaxy tools uses a
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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16 concatenation of the administrator's emails, and the user email, in
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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17 hopes that NCBI will contact all relevant parties should their system be
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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18 abused.
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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20 Additionally, since these are IP level blocks, the Galaxy tool author
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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21 (@erasche) recommends using the following ``jobs_conf.xml`` snippet in
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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22 order to place a system-wide restriction of 1 concurrent Entrez job
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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23 amongst all users.
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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25 .. code:: xml
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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27 <destination id="entrez" runner="local">
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28 </destination>
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29 <limit type="concurrent_jobs" id="entrez">1</limit>
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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30 <tools>
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31 <tool id="ncbi.eutils.efetch" destination="entrez" />
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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32 <tool id="ncbi.eutils.esearch" destination="entrez" />
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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33 <tool id="ncbi.eutils.epost" destination="entrez" />
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34 <tool id="ncbi.eutils.elink" destination="entrez" />
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35 <tool id="ncbi.eutils.einfo" destination="entrez" />
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36 <tool id="ncbi.eutils.esummary" destination="entrez" />
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37 </tools>
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