{bio}[GCCcore/6.4.0] biomart-perl v0.7_e6db561#6745
{bio}[GCCcore/6.4.0] biomart-perl v0.7_e6db561#6745boegel merged 3 commits intoeasybuilders:developfrom
Conversation
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Test report by @vanzod |
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| postinstallcmds = [ | ||
| 'sed -ni "/<MartRegistry>/q;p" %s' % marturlloc, | ||
| 'curl https://useast.ensembl.org/biomart/martservice?type=registry >> %s' % marturlloc, |
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@vanzod Is this some kind of mirror? What does this do exactly?
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Also, why not do this via a patch file?
(we really need better support for runtime patching without relying on sed...)
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That file must be modified based on the content of that URL. I do not see how to do it from a patch...
| 'curl https://useast.ensembl.org/biomart/martservice?type=registry >> %s' % marturlloc, | ||
| ] | ||
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| modloadmsg = "Copy the registry file locally from:\n%(installdir)s/conf/martURLLocation.xml\n\n" |
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The executon of the BioMart Perl scripts requires this file to identify the source URLs for the data. The data is then cached in the same directory where the file is. Hence it needs to reside in a location where the user has write permission.
I will rephrase it.
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Test report by @boegel |
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Test report by @boegel |
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Test report by @boegel |
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Test report by @boegel |
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Going in, thanks @vanzod! |
Requires
#6744