Thanks Assaf.

A couple notes on Galaxy's Cufflinks' wrappers and update checks:

*galaxy-central changeset 4557:eee0e1d344d2, which updated the 
Cufflinks/compare/diff wrappers to support v1.0.* disabled the update check for 
Cufflinks.

*There is no --no-update-check option for for Cuffcompare; I haven't checked to 
see if Cuffcompare actually contacts cufflinks.cbcb.umd.edu before running or 
not.

*galaxy-central changeset 5638:1ab3dfb5d929 disables the update check for 
Cuffdiff.

Best,
J.

On Jun 2, 2011, at 3:33 PM, Assaf Gordon wrote:

> Just FYI,
> 
> 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;
> to:
>   bool no_update_check = true;
> 
> Then recompile and re-install.
> 
> -gordon
> 
> 
> 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.
>> 
>> Best,
>> J.
>> 
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