Hello everybody, I just found out that there was a major update to cufflinks on 5/5/2011. At least for us it now makes no sense anymore to use the old version, besides the fact that the cufflinks team highly recommends upgrading. Does anybody already have new wrappers for all the cuff... tools ready? Do you know if/when the Galaxy codebase will be updated to the new cufflinks version? Best regards, Sarah
Sarah, 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. On May 10, 2011, at 7:53 AM, Sarah Diehl wrote:
Hello everybody,
I just found out that there was a major update to cufflinks on 5/5/2011. At least for us it now makes no sense anymore to use the old version, besides the fact that the cufflinks team highly recommends upgrading. Does anybody already have new wrappers for all the cuff... tools ready? Do you know if/when the Galaxy codebase will be updated to the new cufflinks version?
Best regards, Sarah ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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.
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.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Jeremy, You're right about cuffcompare: it always contacts cufflinks.cbcb.umd.edu. To disable it, change "cuffcompare.cpp" and comment-out line 226 ( "check_version(PACKAGE_VERSION)" ). Thanks, -gordon Jeremy Goecks wrote, On 06/06/2011 10:23 AM:
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.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Assaf Gordon -
Jeremy Goecks -
Sarah Diehl