Mercurial > repos > iuc > ncbi_eutils_elink
comparison README.rst @ 0:59063d2e91c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
| author | iuc |
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| date | Thu, 07 Jul 2016 02:40:20 -0400 |
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| -1:000000000000 | 0:59063d2e91c6 |
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| 1 Galaxy NCBI Entrez Tools | |
| 2 ======================== | |
| 3 | |
| 4 This repo requires a readme as administrators should very aware of some | |
| 5 restrictions NCBI places on the use of the Entrez service. | |
| 6 | |
| 7 NCBI requests that you please limit large jobs to either weekends or | |
| 8 between 9:00 PM and 5:00 AM Eastern time during weekdays. This is not a | |
| 9 request that the Galaxy tool can easily service, so we've included it in | |
| 10 the disclaimer on every tool quite prominently. | |
| 11 | |
| 12 Failure to comply with NCBI's policies may result in an block until | |
| 13 you/the user contacts NCBI and registers the tool ID and their email. | |
| 14 | |
| 15 Note that these are *IP* level blocks so the Galaxy tools uses a | |
| 16 concatenation of the administrator's emails, and the user email, in | |
| 17 hopes that NCBI will contact all relevant parties should their system be | |
| 18 abused. | |
| 19 | |
| 20 Additionally, since these are IP level blocks, the Galaxy tool author | |
| 21 (@erasche) recommends using the following ``jobs_conf.xml`` snippet in | |
| 22 order to place a system-wide restriction of 1 concurrent Entrez job | |
| 23 amongst all users. | |
| 24 | |
| 25 .. code:: xml | |
| 26 | |
| 27 <destination id="entrez" runner="local"> | |
| 28 </destination> | |
| 29 <limit type="concurrent_jobs" id="entrez">1</limit> | |
| 30 <tools> | |
| 31 <tool id="ncbi.eutils.efetch" destination="entrez" /> | |
| 32 <tool id="ncbi.eutils.esearch" destination="entrez" /> | |
| 33 <tool id="ncbi.eutils.epost" destination="entrez" /> | |
| 34 <tool id="ncbi.eutils.elink" destination="entrez" /> | |
| 35 <tool id="ncbi.eutils.einfo" destination="entrez" /> | |
| 36 <tool id="ncbi.eutils.esummary" destination="entrez" /> | |
| 37 </tools> | |
| 38 |