[galaxy-dev] Update of cufflinks
gordon at cshl.edu
Thu Jun 2 15:33:47 EDT 2011
With the recent version of cufflinks (at least 1.0.2), the developers added a 'feature' of automatic version check.
While the idea is nice, the implications are not:
cufflinks,cuffcompare and cuffdiff will connect to host "cufflinks.cbcb.umd.edu" every time you run them.
I'm sure the intentions were good, but I don't like programs "calling home", basically reporting usage statistics and origins.
The "check_update" code is also not written with security in mind, and might be exploited (buffer overruns and such) - it's best to disable it.
This will also generate a message to STDERR, which is just annoying (and bad, with galaxy).
To disable it on the command line, add "--no-update-check" to every invocation.
If you compiled it from source code, edit the file "./src/common.cpp" and change the line:
bool no_update_check = false;
bool no_update_check = true;
Then recompile and re-install.
Jeremy Goecks wrote, On 05/10/2011 09:02 AM:
> We recently updated the Cufflinks/compare/diff wrappers to be compatible with v1.0.* ; the wrappers are available in galaxy-central and should be available in galaxy-dist in the next couple weeks as we're planning another release soon.
> New features in v1.0.* have not been implemented in these updates (and, in fact, there are features from 0.9.* that are still not available); the changes we made were simply to ensure that the wrappers' current functionality works with the new versions.
> In the next couple months we plan to extend the current wrappers to include new functionality. However, community contributions that extend the current wrappers to include new functionality would be most welcome, and we can integrate them into the galaxy code base if/when they are available.
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