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https://github.com/galaxyproject/galaxy.git
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Nicola Soranzo
c852de734d
Fix the following errors:
```
$ python cron/build_chrom_db.py tool-data/shared/ucsc/chrom/ tool-data/shared/ucsc/builds.txt
Retrieving hg38
Failed to retrieve hg38: Problem parsing line ''
Retrieving hg19
Failed to retrieve hg19: Problem parsing line ''
...
```
Broken in commit 9b8e76f9d9 .
This folder holds cron jobs that support galaxy. updateucsc.sh is a shell script to facilitate the updates from UCSC. Galaxy stores several files locally to speed up operations that depend on information from UCSC. These files can all be found in the static/ucsc folder. Before adding updateucsc.sh to the crontab, it is important to note two things. First, updateucsc.sh must be edited to point towards the root galaxy directory. At the top of the file there is a variable "GALAXY" that should be edited. Second, the updates come from UCSC via their table browsers. While the tendency is typically to run cron jobs late at night, UCSC, like most, tend to take down their servers at odd hours for maintenance. The update scripts for UCSC are not CPU intensive, and should be scheduled during normal hours.