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The perl script bed2UCSC.pl below can be used to upload a BED file (custom tracks) to the UCSC wiki track. Feel free to adjust it to your needs. It is licensed under the LGPL 2.1 and all newer versions of the LGPL.
Documentation and Dependencies
The script is documented in the source code. Its usage can be shown using perldoc bed2UCSC.pl. It needs PERL, cURL and an operating system with a /dev/null-device to run. Furthermore the LWP::UserAgent and the Clone module from CPAN have to be available.
Please rename the file to bed2UCSC.pl after downloading from the wiki.
UPDATED: This version of bed2UCSC.pl fixes a problem with pubmed ids.