GBrowse 2.20 released

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GBrowse 2.20 released

Lincoln Stein
Hello Everyone,

I am happy to report that GBrowse 2.20 is now released. You may obtain the package in the following ways:
  1. Install from CPAN: perl -MCPAN 'install Bio::Graphics::Browser2'
  2. Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
  3. Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20 GBrowse-2.20
Here are highlights of the features new in version 2.20:
  • There is a completely revamped user accounts database that allows users to register themselves and manage passwords and other account settings. User accounts provide stable cross-computer storage of track uploads and session settings, can be used for restricting datasources to certain users, and are the basis for community tracks. To migrate accounts from pre 2.20 account databases to the current database, run the gbrowse_metadb_config.pl script (this is also done automatically during "./Build install").
  • Users can elect to turn any uploaded data set into a community track, which the public can then search and view. Users can also share tracks with specific named users, or email links to each other to import tracks casually.
  • A new "details multiplier" option in GBrowse.conf allows rapid mouse panning across the detail panel without loading new data from the server.
  • A draggable ruler now appears in the details panel that can be used to measure the position of features precisely.
  • Uploads now support various flavors of BED and WIG formats, and recognize SAM and BAM file uploads as well.
  • Quantitative wiggle tracks now offer a z-score rescaling option that improves the appearance and interpretability of these tracks. Be sure to use Bio::Graphics version 2.18 or higher for this feature to work correctly.
  • A new authentication plugin framework allows you to integrate GBrowse with enterprise authentication systems such as LDAP and Active Directory. A PamAuthentication plugin connects to the Pluggable Authentcation Modules (PAM) system, which already has interfaces to LDAP, Kerberos, AD and NIS.
In addition, a variety of large and small bugs have been quashed. See the full Changes file for details.

Lincoln

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse 2.20 released

Keiran Raine
Hi Lincoln,

Just tried to build GBrowse 2.20 on our dev machine:

t/06.featuresearch.t ...... "remove_tree" is not exported by the File::Path module
Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9

This same error seems to cause most of the tests to fail.  It's a bit odd though as I know File::Path does export that method.

I'm on perl 5.10.0.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703





On 19 Jan 2011, at 16:40, Lincoln Stein wrote:

Hello Everyone,

I am happy to report that GBrowse 2.20 is now released. You may obtain the package in the following ways:
  1. Install from CPAN: perl -MCPAN 'install Bio::Graphics::Browser2'
  2. Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
  3. Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20 GBrowse-2.20
Here are highlights of the features new in version 2.20:
  • There is a completely revamped user accounts database that allows users to register themselves and manage passwords and other account settings. User accounts provide stable cross-computer storage of track uploads and session settings, can be used for restricting datasources to certain users, and are the basis for community tracks. To migrate accounts from pre 2.20 account databases to the current database, run the gbrowse_metadb_config.pl script (this is also done automatically during "./Build install").
  • Users can elect to turn any uploaded data set into a community track, which the public can then search and view. Users can also share tracks with specific named users, or email links to each other to import tracks casually.
  • A new "details multiplier" option in GBrowse.conf allows rapid mouse panning across the detail panel without loading new data from the server.
  • A draggable ruler now appears in the details panel that can be used to measure the position of features precisely.
  • Uploads now support various flavors of BED and WIG formats, and recognize SAM and BAM file uploads as well.
  • Quantitative wiggle tracks now offer a z-score rescaling option that improves the appearance and interpretability of these tracks. Be sure to use Bio::Graphics version 2.18 or higher for this feature to work correctly.
  • A new authentication plugin framework allows you to integrate GBrowse with enterprise authentication systems such as LDAP and Active Directory. A PamAuthentication plugin connects to the Pluggable Authentcation Modules (PAM) system, which already has interfaces to LDAP, Kerberos, AD and NIS.
In addition, a variety of large and small bugs have been quashed. See the full Changes file for details.

Lincoln

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

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Re: GBrowse 2.20 released

Fields, Christopher J
No, File::Path only exports 'rmtree' and 'mkpath' (old API), not 'remove_tree' (new API).  See under 'Notes':

http://search.cpan.org/perldoc?File::Path

chris

On Jan 19, 2011, at 11:19 AM, Keiran Raine wrote:

> Hi Lincoln,
>
> Just tried to build GBrowse 2.20 on our dev machine:
>
> t/06.featuresearch.t ...... "remove_tree" is not exported by the File::Path module
> Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9
>
> This same error seems to cause most of the tests to fail.  It's a bit odd though as I know File::Path does export that method.
>
> I'm on perl 5.10.0.
>
> Regards,
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> [hidden email]
>
>
>
>
>
> On 19 Jan 2011, at 16:40, Lincoln Stein wrote:
>
>> Hello Everyone,
>>
>> I am happy to report that GBrowse 2.20 is now released. You may obtain the package in the following ways:
>> • Install from CPAN: perl -MCPAN 'install Bio::Graphics::Browser2'
>> • Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
>> • Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20 GBrowse-2.20
>> Here are highlights of the features new in version 2.20:
>> • There is a completely revamped user accounts database that allows users to register themselves and manage passwords and other account settings. User accounts provide stable cross-computer storage of track uploads and session settings, can be used for restricting datasources to certain users, and are the basis for community tracks. To migrate accounts from pre 2.20 account databases to the current database, run the gbrowse_metadb_config.pl script (this is also done automatically during "./Build install").
>> • Users can elect to turn any uploaded data set into a community track, which the public can then search and view. Users can also share tracks with specific named users, or email links to each other to import tracks casually.
>> • A new "details multiplier" option in GBrowse.conf allows rapid mouse panning across the detail panel without loading new data from the server.
>> • A draggable ruler now appears in the details panel that can be used to measure the position of features precisely.
>> • Uploads now support various flavors of BED and WIG formats, and recognize SAM and BAM file uploads as well.
>> • Quantitative wiggle tracks now offer a z-score rescaling option that improves the appearance and interpretability of these tracks. Be sure to use Bio::Graphics version 2.18 or higher for this feature to work correctly.
>> • A new authentication plugin framework allows you to integrate GBrowse with enterprise authentication systems such as LDAP and Active Directory. A PamAuthentication plugin connects to the Pluggable Authentcation Modules (PAM) system, which already has interfaces to LDAP, Kerberos, AD and NIS.
>> In addition, a variety of large and small bugs have been quashed. See the full Changes file for details.
>>
>> Lincoln
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]>
>> ------------------------------------------------------------------------------
>> Protect Your Site and Customers from Malware Attacks
>> Learn about various malware tactics and how to avoid them. Understand
>> malware threats, the impact they can have on your business, and how you
>> can protect your company and customers by using code signing.
>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: GBrowse 2.20 released

Keiran Raine
Hi Chris,

With reference to the actual code though the 'use' directive is  
explicitly exporting the function, as detailed in the 'Notes' section:

use File::Path 'remove_tree';

(line 9 of lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm)

So this should work.

Keiran





On 19 Jan 2011, at 17:28, Chris Fields wrote:

> No, File::Path only exports 'rmtree' and 'mkpath' (old API), not  
> 'remove_tree' (new API).  See under 'Notes':
>
> http://search.cpan.org/perldoc?File::Path
>
> chris
>
> On Jan 19, 2011, at 11:19 AM, Keiran Raine wrote:
>
>> Hi Lincoln,
>>
>> Just tried to build GBrowse 2.20 on our dev machine:
>>
>> t/06.featuresearch.t ...... "remove_tree" is not exported by the  
>> File::Path module
>> Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/
>> t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9
>>
>> This same error seems to cause most of the tests to fail.  It's a  
>> bit odd though as I know File::Path does export that method.
>>
>> I'm on perl 5.10.0.
>>
>> Regards,
>>
>> Keiran Raine
>> Senior Computer Biologist
>> The Cancer Genome Project
>> Ext: 7703
>> [hidden email]
>>
>>
>>
>>
>>
>> On 19 Jan 2011, at 16:40, Lincoln Stein wrote:
>>
>>> Hello Everyone,
>>>
>>> I am happy to report that GBrowse 2.20 is now released. You may  
>>> obtain the package in the following ways:
>>> • Install from CPAN: perl -MCPAN 'install Bio::Graphics::Browser2'
>>> • Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
>>> • Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20 
>>>  GBrowse-2.20
>>> Here are highlights of the features new in version 2.20:
>>> • There is a completely revamped user accounts database that  
>>> allows users to register themselves and manage passwords and other  
>>> account settings. User accounts provide stable cross-computer  
>>> storage of track uploads and session settings, can be used for  
>>> restricting datasources to certain users, and are the basis for  
>>> community tracks. To migrate accounts from pre 2.20 account  
>>> databases to the current database, run the  
>>> gbrowse_metadb_config.pl script (this is also done automatically  
>>> during "./Build install").
>>> • Users can elect to turn any uploaded data set into a community  
>>> track, which the public can then search and view. Users can also  
>>> share tracks with specific named users, or email links to each  
>>> other to import tracks casually.
>>> • A new "details multiplier" option in GBrowse.conf allows rapid  
>>> mouse panning across the detail panel without loading new data  
>>> from the server.
>>> • A draggable ruler now appears in the details panel that can be  
>>> used to measure the position of features precisely.
>>> • Uploads now support various flavors of BED and WIG formats, and  
>>> recognize SAM and BAM file uploads as well.
>>> • Quantitative wiggle tracks now offer a z-score rescaling option  
>>> that improves the appearance and interpretability of these tracks.  
>>> Be sure to use Bio::Graphics version 2.18 or higher for this  
>>> feature to work correctly.
>>> • A new authentication plugin framework allows you to integrate  
>>> GBrowse with enterprise authentication systems such as LDAP and  
>>> Active Directory. A PamAuthentication plugin connects to the  
>>> Pluggable Authentcation Modules (PAM) system, which already has  
>>> interfaces to LDAP, Kerberos, AD and NIS.
>>> In addition, a variety of large and small bugs have been quashed.  
>>> See the full Changes file for details.
>>>
>>> Lincoln
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]>
>>> ------------------------------------------------------------------------------
>>> Protect Your Site and Customers from Malware Attacks
>>> Learn about various malware tactics and how to avoid them.  
>>> Understand
>>> malware threats, the impact they can have on your business, and  
>>> how you
>>> can protect your company and customers by using code signing.
>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>> -- The Wellcome Trust Sanger Institute is operated by Genome  
>> Research Limited, a charity registered in England with number  
>> 1021457 and a compa ny registered in England with number 2742969,  
>> whose registered office is 2 15 Euston Road, London, NW1 2BE.
>> ------------------------------------------------------------------------------
>> Protect Your Site and Customers from Malware Attacks
>> Learn about various malware tactics and how to avoid them. Understand
>> malware threats, the impact they can have on your business, and how  
>> you
>> can protect your company and customers by using code signing.
>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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Learn about various malware tactics and how to avoid them. Understand
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can protect your company and customers by using code signing.
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Re: GBrowse 2.20 released

Fields, Christopher J
Odd, then.  

Actually, after re-reading that the error indicates the version of File::Path being used doesn't export 'remove_path', so the issue may not be with GBrowse but possibly an old version of File::Path mucking things up.  Have you tried to reinstall File::Path?  Depending on how your install was set up, you might need to use 'sudo'.

chris

On Jan 19, 2011, at 11:47 AM, Keiran Raine wrote:

> Hi Chris,
>
> With reference to the actual code though the 'use' directive is  
> explicitly exporting the function, as detailed in the 'Notes' section:
>
> use File::Path 'remove_tree';
>
> (line 9 of lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm)
>
> So this should work.
>
> Keiran
>
>
>
>
>
> On 19 Jan 2011, at 17:28, Chris Fields wrote:
>
>> No, File::Path only exports 'rmtree' and 'mkpath' (old API), not  
>> 'remove_tree' (new API).  See under 'Notes':
>>
>> http://search.cpan.org/perldoc?File::Path
>>
>> chris
>>
>> On Jan 19, 2011, at 11:19 AM, Keiran Raine wrote:
>>
>>> Hi Lincoln,
>>>
>>> Just tried to build GBrowse 2.20 on our dev machine:
>>>
>>> t/06.featuresearch.t ...... "remove_tree" is not exported by the  
>>> File::Path module
>>> Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/
>>> t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9
>>>
>>> This same error seems to cause most of the tests to fail.  It's a  
>>> bit odd though as I know File::Path does export that method.
>>>
>>> I'm on perl 5.10.0.
>>>
>>> Regards,
>>>
>>> Keiran Raine
>>> Senior Computer Biologist
>>> The Cancer Genome Project
>>> Ext: 7703
>>> [hidden email]
>>>
>>>
>>>
>>>
>>>
>>> On 19 Jan 2011, at 16:40, Lincoln Stein wrote:
>>>
>>>> Hello Everyone,
>>>>
>>>> I am happy to report that GBrowse 2.20 is now released. You may  
>>>> obtain the package in the following ways:
>>>> • Install from CPAN: perl -MCPAN 'install Bio::Graphics::Browser2'
>>>> • Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
>>>> • Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20 
>>>> GBrowse-2.20
>>>> Here are highlights of the features new in version 2.20:
>>>> • There is a completely revamped user accounts database that  
>>>> allows users to register themselves and manage passwords and other  
>>>> account settings. User accounts provide stable cross-computer  
>>>> storage of track uploads and session settings, can be used for  
>>>> restricting datasources to certain users, and are the basis for  
>>>> community tracks. To migrate accounts from pre 2.20 account  
>>>> databases to the current database, run the  
>>>> gbrowse_metadb_config.pl script (this is also done automatically  
>>>> during "./Build install").
>>>> • Users can elect to turn any uploaded data set into a community  
>>>> track, which the public can then search and view. Users can also  
>>>> share tracks with specific named users, or email links to each  
>>>> other to import tracks casually.
>>>> • A new "details multiplier" option in GBrowse.conf allows rapid  
>>>> mouse panning across the detail panel without loading new data  
>>>> from the server.
>>>> • A draggable ruler now appears in the details panel that can be  
>>>> used to measure the position of features precisely.
>>>> • Uploads now support various flavors of BED and WIG formats, and  
>>>> recognize SAM and BAM file uploads as well.
>>>> • Quantitative wiggle tracks now offer a z-score rescaling option  
>>>> that improves the appearance and interpretability of these tracks.  
>>>> Be sure to use Bio::Graphics version 2.18 or higher for this  
>>>> feature to work correctly.
>>>> • A new authentication plugin framework allows you to integrate  
>>>> GBrowse with enterprise authentication systems such as LDAP and  
>>>> Active Directory. A PamAuthentication plugin connects to the  
>>>> Pluggable Authentcation Modules (PAM) system, which already has  
>>>> interfaces to LDAP, Kerberos, AD and NIS.
>>>> In addition, a variety of large and small bugs have been quashed.  
>>>> See the full Changes file for details.
>>>>
>>>> Lincoln
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <[hidden email]>
>>>> ------------------------------------------------------------------------------
>>>> Protect Your Site and Customers from Malware Attacks
>>>> Learn about various malware tactics and how to avoid them.  
>>>> Understand
>>>> malware threats, the impact they can have on your business, and  
>>>> how you
>>>> can protect your company and customers by using code signing.
>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>> -- The Wellcome Trust Sanger Institute is operated by Genome  
>>> Research Limited, a charity registered in England with number  
>>> 1021457 and a compa ny registered in England with number 2742969,  
>>> whose registered office is 2 15 Euston Road, London, NW1 2BE.
>>> ------------------------------------------------------------------------------
>>> Protect Your Site and Customers from Malware Attacks
>>> Learn about various malware tactics and how to avoid them. Understand
>>> malware threats, the impact they can have on your business, and how  
>>> you
>>> can protect your company and customers by using code signing.
>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: GBrowse 2.20 released

Keiran Raine
I can try to install it to our prefix location but the core module  
already installed is 2.04:

~> /usr/bin/perl -le 'eval "require $ARGV[0]" and print $ARGV[0]-
 >VERSION' File::Path
2.04

Keiran

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703
[hidden email]





On 19 Jan 2011, at 18:15, Chris Fields wrote:

> Odd, then.
>
> Actually, after re-reading that the error indicates the version of  
> File::Path being used doesn't export 'remove_path', so the issue may  
> not be with GBrowse but possibly an old version of File::Path  
> mucking things up.  Have you tried to reinstall File::Path?  
> Depending on how your install was set up, you might need to use  
> 'sudo'.
>
> chris
>
> On Jan 19, 2011, at 11:47 AM, Keiran Raine wrote:
>
>> Hi Chris,
>>
>> With reference to the actual code though the 'use' directive is
>> explicitly exporting the function, as detailed in the 'Notes'  
>> section:
>>
>> use File::Path 'remove_tree';
>>
>> (line 9 of lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm)
>>
>> So this should work.
>>
>> Keiran
>>
>>
>>
>>
>>
>> On 19 Jan 2011, at 17:28, Chris Fields wrote:
>>
>>> No, File::Path only exports 'rmtree' and 'mkpath' (old API), not
>>> 'remove_tree' (new API).  See under 'Notes':
>>>
>>> http://search.cpan.org/perldoc?File::Path
>>>
>>> chris
>>>
>>> On Jan 19, 2011, at 11:19 AM, Keiran Raine wrote:
>>>
>>>> Hi Lincoln,
>>>>
>>>> Just tried to build GBrowse 2.20 on our dev machine:
>>>>
>>>> t/06.featuresearch.t ...... "remove_tree" is not exported by the
>>>> File::Path module
>>>> Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/
>>>> t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9
>>>>
>>>> This same error seems to cause most of the tests to fail.  It's a
>>>> bit odd though as I know File::Path does export that method.
>>>>
>>>> I'm on perl 5.10.0.
>>>>
>>>> Regards,
>>>>
>>>> Keiran Raine
>>>> Senior Computer Biologist
>>>> The Cancer Genome Project
>>>> Ext: 7703
>>>> [hidden email]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 19 Jan 2011, at 16:40, Lincoln Stein wrote:
>>>>
>>>>> Hello Everyone,
>>>>>
>>>>> I am happy to report that GBrowse 2.20 is now released. You may
>>>>> obtain the package in the following ways:
>>>>> • Install from CPAN: perl -MCPAN 'install  
>>>>> Bio::Graphics::Browser2'
>>>>> • Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
>>>>> • Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20
>>>>> GBrowse-2.20
>>>>> Here are highlights of the features new in version 2.20:
>>>>> • There is a completely revamped user accounts database that
>>>>> allows users to register themselves and manage passwords and other
>>>>> account settings. User accounts provide stable cross-computer
>>>>> storage of track uploads and session settings, can be used for
>>>>> restricting datasources to certain users, and are the basis for
>>>>> community tracks. To migrate accounts from pre 2.20 account
>>>>> databases to the current database, run the
>>>>> gbrowse_metadb_config.pl script (this is also done automatically
>>>>> during "./Build install").
>>>>> • Users can elect to turn any uploaded data set into a community
>>>>> track, which the public can then search and view. Users can also
>>>>> share tracks with specific named users, or email links to each
>>>>> other to import tracks casually.
>>>>> • A new "details multiplier" option in GBrowse.conf allows rapid
>>>>> mouse panning across the detail panel without loading new data
>>>>> from the server.
>>>>> • A draggable ruler now appears in the details panel that can be
>>>>> used to measure the position of features precisely.
>>>>> • Uploads now support various flavors of BED and WIG formats, and
>>>>> recognize SAM and BAM file uploads as well.
>>>>> • Quantitative wiggle tracks now offer a z-score rescaling option
>>>>> that improves the appearance and interpretability of these tracks.
>>>>> Be sure to use Bio::Graphics version 2.18 or higher for this
>>>>> feature to work correctly.
>>>>> • A new authentication plugin framework allows you to integrate
>>>>> GBrowse with enterprise authentication systems such as LDAP and
>>>>> Active Directory. A PamAuthentication plugin connects to the
>>>>> Pluggable Authentcation Modules (PAM) system, which already has
>>>>> interfaces to LDAP, Kerberos, AD and NIS.
>>>>> In addition, a variety of large and small bugs have been quashed.
>>>>> See the full Changes file for details.
>>>>>
>>>>> Lincoln
>>>>>
>>>>> --
>>>>> Lincoln D. Stein
>>>>> Director, Informatics and Biocomputing Platform
>>>>> Ontario Institute for Cancer Research
>>>>> 101 College St., Suite 800
>>>>> Toronto, ON, Canada M5G0A3
>>>>> 416 673-8514
>>>>> Assistant: Renata Musa <[hidden email]>
>>>>> ------------------------------------------------------------------------------
>>>>> Protect Your Site and Customers from Malware Attacks
>>>>> Learn about various malware tactics and how to avoid them.
>>>>> Understand
>>>>> malware threats, the impact they can have on your business, and
>>>>> how you
>>>>> can protect your company and customers by using code signing.
>>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>> -- The Wellcome Trust Sanger Institute is operated by Genome  
>>>> Research Limited, a charity registered in England with number
>>>> 1021457 and a compa ny registered in England with number 2742969,
>>>> whose registered office is 2 15 Euston Road, London, NW1 2BE.
>>>> ------------------------------------------------------------------------------
>>>> Protect Your Site and Customers from Malware Attacks
>>>> Learn about various malware tactics and how to avoid them.  
>>>> Understand
>>>> malware threats, the impact they can have on your business, and how
>>>> you
>>>> can protect your company and customers by using code signing.
>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>>
>> ------------------------------------------------------------------------------
>> Protect Your Site and Customers from Malware Attacks
>> Learn about various malware tactics and how to avoid them. Understand
>> malware threats, the impact they can have on your business, and how  
>> you
>> can protect your company and customers by using code signing.
>> http://p.sf.net/sfu/oracle-sfdevnl
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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Re: GBrowse 2.20 released

Keiran Raine
Hi Chris,

Installing File::Path (2.08) got past that problem but now there is a  
problem with:

lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm

t/07.karyotype.t .......... Base class package  
"Bio::Graphics::FeatureFile" is empty.
     (Perhaps you need to 'use' the module which defines that package  
first.)
  at /var/tmp/kr2/GBrowse-2.20/t/../lib/Bio/Graphics/Browser2/
AuthorizedFeatureFile.pm line 5

I've already pre-installed Bio-Graphics 2.18 as instructed in  
Lincoln's original email.

I don't normally have this many problems testing new versions.....(and  
I've been doing it for 15 months)

Keiran





On 19 Jan 2011, at 18:22, Keiran Raine wrote:

> I can try to install it to our prefix location but the core module
> already installed is 2.04:
>
> ~> /usr/bin/perl -le 'eval "require $ARGV[0]" and print $ARGV[0]-
>> VERSION' File::Path
> 2.04
>
> Keiran
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> [hidden email]
>
>
>
>
>
> On 19 Jan 2011, at 18:15, Chris Fields wrote:
>
>> Odd, then.
>>
>> Actually, after re-reading that the error indicates the version of
>> File::Path being used doesn't export 'remove_path', so the issue may
>> not be with GBrowse but possibly an old version of File::Path
>> mucking things up.  Have you tried to reinstall File::Path?
>> Depending on how your install was set up, you might need to use
>> 'sudo'.
>>
>> chris
>>
>> On Jan 19, 2011, at 11:47 AM, Keiran Raine wrote:
>>
>>> Hi Chris,
>>>
>>> With reference to the actual code though the 'use' directive is
>>> explicitly exporting the function, as detailed in the 'Notes'
>>> section:
>>>
>>> use File::Path 'remove_tree';
>>>
>>> (line 9 of lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm)
>>>
>>> So this should work.
>>>
>>> Keiran
>>>
>>>
>>>
>>>
>>>
>>> On 19 Jan 2011, at 17:28, Chris Fields wrote:
>>>
>>>> No, File::Path only exports 'rmtree' and 'mkpath' (old API), not
>>>> 'remove_tree' (new API).  See under 'Notes':
>>>>
>>>> http://search.cpan.org/perldoc?File::Path
>>>>
>>>> chris
>>>>
>>>> On Jan 19, 2011, at 11:19 AM, Keiran Raine wrote:
>>>>
>>>>> Hi Lincoln,
>>>>>
>>>>> Just tried to build GBrowse 2.20 on our dev machine:
>>>>>
>>>>> t/06.featuresearch.t ...... "remove_tree" is not exported by the
>>>>> File::Path module
>>>>> Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/
>>>>> t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9
>>>>>
>>>>> This same error seems to cause most of the tests to fail.  It's a
>>>>> bit odd though as I know File::Path does export that method.
>>>>>
>>>>> I'm on perl 5.10.0.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Keiran Raine
>>>>> Senior Computer Biologist
>>>>> The Cancer Genome Project
>>>>> Ext: 7703
>>>>> [hidden email]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 19 Jan 2011, at 16:40, Lincoln Stein wrote:
>>>>>
>>>>>> Hello Everyone,
>>>>>>
>>>>>> I am happy to report that GBrowse 2.20 is now released. You may
>>>>>> obtain the package in the following ways:
>>>>>> • Install from CPAN: perl -MCPAN 'install
>>>>>> Bio::Graphics::Browser2'
>>>>>> • Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
>>>>>> • Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20
>>>>>> GBrowse-2.20
>>>>>> Here are highlights of the features new in version 2.20:
>>>>>> • There is a completely revamped user accounts database that
>>>>>> allows users to register themselves and manage passwords and  
>>>>>> other
>>>>>> account settings. User accounts provide stable cross-computer
>>>>>> storage of track uploads and session settings, can be used for
>>>>>> restricting datasources to certain users, and are the basis for
>>>>>> community tracks. To migrate accounts from pre 2.20 account
>>>>>> databases to the current database, run the
>>>>>> gbrowse_metadb_config.pl script (this is also done automatically
>>>>>> during "./Build install").
>>>>>> • Users can elect to turn any uploaded data set into a community
>>>>>> track, which the public can then search and view. Users can also
>>>>>> share tracks with specific named users, or email links to each
>>>>>> other to import tracks casually.
>>>>>> • A new "details multiplier" option in GBrowse.conf allows rapid
>>>>>> mouse panning across the detail panel without loading new data
>>>>>> from the server.
>>>>>> • A draggable ruler now appears in the details panel that can be
>>>>>> used to measure the position of features precisely.
>>>>>> • Uploads now support various flavors of BED and WIG formats,  
>>>>>> and
>>>>>> recognize SAM and BAM file uploads as well.
>>>>>> • Quantitative wiggle tracks now offer a z-score rescaling  
>>>>>> option
>>>>>> that improves the appearance and interpretability of these  
>>>>>> tracks.
>>>>>> Be sure to use Bio::Graphics version 2.18 or higher for this
>>>>>> feature to work correctly.
>>>>>> • A new authentication plugin framework allows you to integrate
>>>>>> GBrowse with enterprise authentication systems such as LDAP and
>>>>>> Active Directory. A PamAuthentication plugin connects to the
>>>>>> Pluggable Authentcation Modules (PAM) system, which already has
>>>>>> interfaces to LDAP, Kerberos, AD and NIS.
>>>>>> In addition, a variety of large and small bugs have been quashed.
>>>>>> See the full Changes file for details.
>>>>>>
>>>>>> Lincoln
>>>>>>
>>>>>> --
>>>>>> Lincoln D. Stein
>>>>>> Director, Informatics and Biocomputing Platform
>>>>>> Ontario Institute for Cancer Research
>>>>>> 101 College St., Suite 800
>>>>>> Toronto, ON, Canada M5G0A3
>>>>>> 416 673-8514
>>>>>> Assistant: Renata Musa <[hidden email]>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Protect Your Site and Customers from Malware Attacks
>>>>>> Learn about various malware tactics and how to avoid them.
>>>>>> Understand
>>>>>> malware threats, the impact they can have on your business, and
>>>>>> how you
>>>>>> can protect your company and customers by using code signing.
>>>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>> -- The Wellcome Trust Sanger Institute is operated by Genome  
>>>>> Research Limited, a charity registered in England with number
>>>>> 1021457 and a compa ny registered in England with number 2742969,
>>>>> whose registered office is 2 15 Euston Road, London, NW1 2BE.
>>>>> ------------------------------------------------------------------------------
>>>>> Protect Your Site and Customers from Malware Attacks
>>>>> Learn about various malware tactics and how to avoid them.
>>>>> Understand
>>>>> malware threats, the impact they can have on your business, and  
>>>>> how
>>>>> you
>>>>> can protect your company and customers by using code signing.
>>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>>
>>> ------------------------------------------------------------------------------
>>> Protect Your Site and Customers from Malware Attacks
>>> Learn about various malware tactics and how to avoid them.  
>>> Understand
>>> malware threats, the impact they can have on your business, and how
>>> you
>>> can protect your company and customers by using code signing.
>>> http://p.sf.net/sfu/oracle-sfdevnl
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how  
> you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Protect Your Site and Customers from Malware Attacks
Learn about various malware tactics and how to avoid them. Understand
malware threats, the impact they can have on your business, and how you
can protect your company and customers by using code signing.
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
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Re: GBrowse 2.20 released

Lincoln Stein
Hi Keiran, et al,

This all seems to be perl version problems, probably easy to fix. I will work on this and release 2.21 within 24 h.

Lincoln

On Wed, Jan 19, 2011 at 1:33 PM, Keiran Raine <[hidden email]> wrote:
Hi Chris,

Installing File::Path (2.08) got past that problem but now there is a
problem with:

lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm

t/07.karyotype.t .......... Base class package
"Bio::Graphics::FeatureFile" is empty.
    (Perhaps you need to 'use' the module which defines that package
first.)
 at /var/tmp/kr2/GBrowse-2.20/t/../lib/Bio/Graphics/Browser2/
AuthorizedFeatureFile.pm line 5

I've already pre-installed Bio-Graphics 2.18 as instructed in
Lincoln's original email.

I don't normally have this many problems testing new versions.....(and
I've been doing it for 15 months)

Keiran





On 19 Jan 2011, at 18:22, Keiran Raine wrote:

> I can try to install it to our prefix location but the core module
> already installed is 2.04:
>
> ~> /usr/bin/perl -le 'eval "require $ARGV[0]" and print $ARGV[0]-
>> VERSION' File::Path
> 2.04
>
> Keiran
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> [hidden email]
>
>
>
>
>
> On 19 Jan 2011, at 18:15, Chris Fields wrote:
>
>> Odd, then.
>>
>> Actually, after re-reading that the error indicates the version of
>> File::Path being used doesn't export 'remove_path', so the issue may
>> not be with GBrowse but possibly an old version of File::Path
>> mucking things up.  Have you tried to reinstall File::Path?
>> Depending on how your install was set up, you might need to use
>> 'sudo'.
>>
>> chris
>>
>> On Jan 19, 2011, at 11:47 AM, Keiran Raine wrote:
>>
>>> Hi Chris,
>>>
>>> With reference to the actual code though the 'use' directive is
>>> explicitly exporting the function, as detailed in the 'Notes'
>>> section:
>>>
>>> use File::Path 'remove_tree';
>>>
>>> (line 9 of lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm)
>>>
>>> So this should work.
>>>
>>> Keiran
>>>
>>>
>>>
>>>
>>>
>>> On 19 Jan 2011, at 17:28, Chris Fields wrote:
>>>
>>>> No, File::Path only exports 'rmtree' and 'mkpath' (old API), not
>>>> 'remove_tree' (new API).  See under 'Notes':
>>>>
>>>> http://search.cpan.org/perldoc?File::Path
>>>>
>>>> chris
>>>>
>>>> On Jan 19, 2011, at 11:19 AM, Keiran Raine wrote:
>>>>
>>>>> Hi Lincoln,
>>>>>
>>>>> Just tried to build GBrowse 2.20 on our dev machine:
>>>>>
>>>>> t/06.featuresearch.t ...... "remove_tree" is not exported by the
>>>>> File::Path module
>>>>> Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/
>>>>> t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9
>>>>>
>>>>> This same error seems to cause most of the tests to fail.  It's a
>>>>> bit odd though as I know File::Path does export that method.
>>>>>
>>>>> I'm on perl 5.10.0.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Keiran Raine
>>>>> Senior Computer Biologist
>>>>> The Cancer Genome Project
>>>>> Ext: 7703
>>>>> [hidden email]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 19 Jan 2011, at 16:40, Lincoln Stein wrote:
>>>>>
>>>>>> Hello Everyone,
>>>>>>
>>>>>> I am happy to report that GBrowse 2.20 is now released. You may
>>>>>> obtain the package in the following ways:
>>>>>>  • Install from CPAN: perl -MCPAN 'install
>>>>>> Bio::Graphics::Browser2'
>>>>>>  • Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
>>>>>>  • Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20
>>>>>> GBrowse-2.20
>>>>>> Here are highlights of the features new in version 2.20:
>>>>>>  • There is a completely revamped user accounts database that
>>>>>> allows users to register themselves and manage passwords and
>>>>>> other
>>>>>> account settings. User accounts provide stable cross-computer
>>>>>> storage of track uploads and session settings, can be used for
>>>>>> restricting datasources to certain users, and are the basis for
>>>>>> community tracks. To migrate accounts from pre 2.20 account
>>>>>> databases to the current database, run the
>>>>>> gbrowse_metadb_config.pl script (this is also done automatically
>>>>>> during "./Build install").
>>>>>>  • Users can elect to turn any uploaded data set into a community
>>>>>> track, which the public can then search and view. Users can also
>>>>>> share tracks with specific named users, or email links to each
>>>>>> other to import tracks casually.
>>>>>>  • A new "details multiplier" option in GBrowse.conf allows rapid
>>>>>> mouse panning across the detail panel without loading new data
>>>>>> from the server.
>>>>>>  • A draggable ruler now appears in the details panel that can be
>>>>>> used to measure the position of features precisely.
>>>>>>  • Uploads now support various flavors of BED and WIG formats,
>>>>>> and
>>>>>> recognize SAM and BAM file uploads as well.
>>>>>>  • Quantitative wiggle tracks now offer a z-score rescaling
>>>>>> option
>>>>>> that improves the appearance and interpretability of these
>>>>>> tracks.
>>>>>> Be sure to use Bio::Graphics version 2.18 or higher for this
>>>>>> feature to work correctly.
>>>>>>  • A new authentication plugin framework allows you to integrate
>>>>>> GBrowse with enterprise authentication systems such as LDAP and
>>>>>> Active Directory. A PamAuthentication plugin connects to the
>>>>>> Pluggable Authentcation Modules (PAM) system, which already has
>>>>>> interfaces to LDAP, Kerberos, AD and NIS.
>>>>>> In addition, a variety of large and small bugs have been quashed.
>>>>>> See the full Changes file for details.
>>>>>>
>>>>>> Lincoln
>>>>>>
>>>>>> --
>>>>>> Lincoln D. Stein
>>>>>> Director, Informatics and Biocomputing Platform
>>>>>> Ontario Institute for Cancer Research
>>>>>> 101 College St., Suite 800
>>>>>> Toronto, ON, Canada M5G0A3
>>>>>> 416 673-8514
>>>>>> Assistant: Renata Musa <[hidden email]>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Protect Your Site and Customers from Malware Attacks
>>>>>> Learn about various malware tactics and how to avoid them.
>>>>>> Understand
>>>>>> malware threats, the impact they can have on your business, and
>>>>>> how you
>>>>>> can protect your company and customers by using code signing.
>>>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>> -- The Wellcome Trust Sanger Institute is operated by Genome
>>>>> Research Limited, a charity registered in England with number
>>>>> 1021457 and a compa ny registered in England with number 2742969,
>>>>> whose registered office is 2 15 Euston Road, London, NW1 2BE.
>>>>> ------------------------------------------------------------------------------
>>>>> Protect Your Site and Customers from Malware Attacks
>>>>> Learn about various malware tactics and how to avoid them.
>>>>> Understand
>>>>> malware threats, the impact they can have on your business, and
>>>>> how
>>>>> you
>>>>> can protect your company and customers by using code signing.
>>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>>
>>> ------------------------------------------------------------------------------
>>> Protect Your Site and Customers from Malware Attacks
>>> Learn about various malware tactics and how to avoid them.
>>> Understand
>>> malware threats, the impact they can have on your business, and how
>>> you
>>> can protect your company and customers by using code signing.
>>> http://p.sf.net/sfu/oracle-sfdevnl
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how
> you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Protect Your Site and Customers from Malware Attacks
Learn about various malware tactics and how to avoid them. Understand
malware threats, the impact they can have on your business, and how you
can protect your company and customers by using code signing.
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Protect Your Site and Customers from Malware Attacks
Learn about various malware tactics and how to avoid them. Understand
malware threats, the impact they can have on your business, and how you
can protect your company and customers by using code signing.
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
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Re: GBrowse 2.20 released

Lincoln Stein-2
In reply to this post by Keiran Raine
Hi Keiran, et al,

I've changed all the calls to remove_tree to rmtree. Sorry about that. 

I am stumped by the Bio::Graphics::FeatureFile error, however. Tests 01-06 have the same dependency on Bio::Graphics::FeatureFile that test 07 does, and it puzzles me that 07 should fail. Have you made any headway on this?

Lincoln

On Wed, Jan 19, 2011 at 1:33 PM, Keiran Raine <[hidden email]> wrote:
Hi Chris,

Installing File::Path (2.08) got past that problem but now there is a
problem with:

lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm

t/07.karyotype.t .......... Base class package
"Bio::Graphics::FeatureFile" is empty.
    (Perhaps you need to 'use' the module which defines that package
first.)
 at /var/tmp/kr2/GBrowse-2.20/t/../lib/Bio/Graphics/Browser2/
AuthorizedFeatureFile.pm line 5

I've already pre-installed Bio-Graphics 2.18 as instructed in
Lincoln's original email.

I don't normally have this many problems testing new versions.....(and
I've been doing it for 15 months)

Keiran





On 19 Jan 2011, at 18:22, Keiran Raine wrote:

> I can try to install it to our prefix location but the core module
> already installed is 2.04:
>
> ~> /usr/bin/perl -le 'eval "require $ARGV[0]" and print $ARGV[0]-
>> VERSION' File::Path
> 2.04
>
> Keiran
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> [hidden email]
>
>
>
>
>
> On 19 Jan 2011, at 18:15, Chris Fields wrote:
>
>> Odd, then.
>>
>> Actually, after re-reading that the error indicates the version of
>> File::Path being used doesn't export 'remove_path', so the issue may
>> not be with GBrowse but possibly an old version of File::Path
>> mucking things up.  Have you tried to reinstall File::Path?
>> Depending on how your install was set up, you might need to use
>> 'sudo'.
>>
>> chris
>>
>> On Jan 19, 2011, at 11:47 AM, Keiran Raine wrote:
>>
>>> Hi Chris,
>>>
>>> With reference to the actual code though the 'use' directive is
>>> explicitly exporting the function, as detailed in the 'Notes'
>>> section:
>>>
>>> use File::Path 'remove_tree';
>>>
>>> (line 9 of lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm)
>>>
>>> So this should work.
>>>
>>> Keiran
>>>
>>>
>>>
>>>
>>>
>>> On 19 Jan 2011, at 17:28, Chris Fields wrote:
>>>
>>>> No, File::Path only exports 'rmtree' and 'mkpath' (old API), not
>>>> 'remove_tree' (new API).  See under 'Notes':
>>>>
>>>> http://search.cpan.org/perldoc?File::Path
>>>>
>>>> chris
>>>>
>>>> On Jan 19, 2011, at 11:19 AM, Keiran Raine wrote:
>>>>
>>>>> Hi Lincoln,
>>>>>
>>>>> Just tried to build GBrowse 2.20 on our dev machine:
>>>>>
>>>>> t/06.featuresearch.t ...... "remove_tree" is not exported by the
>>>>> File::Path module
>>>>> Can't continue after import errors at /var/tmp/kr2/GBrowse-2.20/
>>>>> t/../lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm line 9
>>>>>
>>>>> This same error seems to cause most of the tests to fail.  It's a
>>>>> bit odd though as I know File::Path does export that method.
>>>>>
>>>>> I'm on perl 5.10.0.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Keiran Raine
>>>>> Senior Computer Biologist
>>>>> The Cancer Genome Project
>>>>> Ext: 7703
>>>>> [hidden email]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 19 Jan 2011, at 16:40, Lincoln Stein wrote:
>>>>>
>>>>>> Hello Everyone,
>>>>>>
>>>>>> I am happy to report that GBrowse 2.20 is now released. You may
>>>>>> obtain the package in the following ways:
>>>>>>  • Install from CPAN: perl -MCPAN 'install
>>>>>> Bio::Graphics::Browser2'
>>>>>>  • Download the source code from Sourceforge at https://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.20/
>>>>>>  • Checkout tag release-2_20 from the Sourceforge SVN: svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/tags/release-2_20
>>>>>> GBrowse-2.20
>>>>>> Here are highlights of the features new in version 2.20:
>>>>>>  • There is a completely revamped user accounts database that
>>>>>> allows users to register themselves and manage passwords and
>>>>>> other
>>>>>> account settings. User accounts provide stable cross-computer
>>>>>> storage of track uploads and session settings, can be used for
>>>>>> restricting datasources to certain users, and are the basis for
>>>>>> community tracks. To migrate accounts from pre 2.20 account
>>>>>> databases to the current database, run the
>>>>>> gbrowse_metadb_config.pl script (this is also done automatically
>>>>>> during "./Build install").
>>>>>>  • Users can elect to turn any uploaded data set into a community
>>>>>> track, which the public can then search and view. Users can also
>>>>>> share tracks with specific named users, or email links to each
>>>>>> other to import tracks casually.
>>>>>>  • A new "details multiplier" option in GBrowse.conf allows rapid
>>>>>> mouse panning across the detail panel without loading new data
>>>>>> from the server.
>>>>>>  • A draggable ruler now appears in the details panel that can be
>>>>>> used to measure the position of features precisely.
>>>>>>  • Uploads now support various flavors of BED and WIG formats,
>>>>>> and
>>>>>> recognize SAM and BAM file uploads as well.
>>>>>>  • Quantitative wiggle tracks now offer a z-score rescaling
>>>>>> option
>>>>>> that improves the appearance and interpretability of these
>>>>>> tracks.
>>>>>> Be sure to use Bio::Graphics version 2.18 or higher for this
>>>>>> feature to work correctly.
>>>>>>  • A new authentication plugin framework allows you to integrate
>>>>>> GBrowse with enterprise authentication systems such as LDAP and
>>>>>> Active Directory. A PamAuthentication plugin connects to the
>>>>>> Pluggable Authentcation Modules (PAM) system, which already has
>>>>>> interfaces to LDAP, Kerberos, AD and NIS.
>>>>>> In addition, a variety of large and small bugs have been quashed.
>>>>>> See the full Changes file for details.
>>>>>>
>>>>>> Lincoln
>>>>>>
>>>>>> --
>>>>>> Lincoln D. Stein
>>>>>> Director, Informatics and Biocomputing Platform
>>>>>> Ontario Institute for Cancer Research
>>>>>> 101 College St., Suite 800
>>>>>> Toronto, ON, Canada M5G0A3
>>>>>> 416 673-8514
>>>>>> Assistant: Renata Musa <[hidden email]>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Protect Your Site and Customers from Malware Attacks
>>>>>> Learn about various malware tactics and how to avoid them.
>>>>>> Understand
>>>>>> malware threats, the impact they can have on your business, and
>>>>>> how you
>>>>>> can protect your company and customers by using code signing.
>>>>>> http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>> -- The Wellcome Trust Sanger Institute is operated by Genome
>>>>> Research Limited, a charity registered in England with number
>>>>> 1021457 and a compa ny registered in England with number 2742969,
>>>>> whose registered office is 2 15 Euston Road, London, NW1 2BE.
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>>>
>>>
>>>
>>> --
>>> The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>>
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>>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
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 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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416 673-8514
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Re: GBrowse 2.20 released

Keiran Raine
On 20 Jan 2011, at 18:35, Lincoln Stein wrote:

> Hi Keiran, et al,
>
> I've changed all the calls to remove_tree to rmtree. Sorry about that.
>
> I am stumped by the Bio::Graphics::FeatureFile error, however. Tests  
> 01-06 have the same dependency on Bio::Graphics::FeatureFile that  
> test 07 does, and it puzzles me that 07 should fail. Have you made  
> any headway on this?

Ah, the others failed also I just chose one...

I have subsequently identified that there was an earlier error saying  
Capture::Tiny was not found.  I've re installed this and now I have  
the File::Path problem back, and this time I can't get it to go away.

Is it only Filesystem.pm that will need changing for remove_tree calls  
(and the explicit export)?  If so I'll modify it and see if my issues  
are resolved.

>
> Lincoln



--
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 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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Re: GBrowse 2.20 released

Lincoln Stein-2
There are two files that need modification: Filesystem.pm, and bin/gbrowse_metadb_config.pl

With respect to the Bio::Graphics::FeatureFile error, what do you get when you run this from the command line:

   perl -MBio::Graphics::FeatureFile -e 0

What does running this script give you:

 #!/usr/bin/perl
 use strict;
 use warnings;

 print Foo->new;
 exit 0;

 package Foo;
 use base 'Bio::Graphics::FeatureFile';
 sub new {
    my $class = shift;
    warn $class,': new()';
    return $class->SUPER::new(@_);
 }

On Thu, Jan 20, 2011 at 1:48 PM, Keiran Raine <[hidden email]> wrote:
On 20 Jan 2011, at 18:35, Lincoln Stein wrote:

Hi Keiran, et al,

I've changed all the calls to remove_tree to rmtree. Sorry about that.

I am stumped by the Bio::Graphics::FeatureFile error, however. Tests 01-06 have the same dependency on Bio::Graphics::FeatureFile that test 07 does, and it puzzles me that 07 should fail. Have you made any headway on this?

Ah, the others failed also I just chose one...

I have subsequently identified that there was an earlier error saying Capture::Tiny was not found.  I've re installed this and now I have the File::Path problem back, and this time I can't get it to go away.

Is it only Filesystem.pm that will need changing for remove_tree calls (and the explicit export)?  If so I'll modify it and see if my issues are resolved.


Lincoln



--
The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE.



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: GBrowse 2.20 released

Keiran Raine
On 20 Jan 2011, at 18:55, Lincoln Stein wrote:

There are two files that need modification: Filesystem.pm, and bin/gbrowse_metadb_config.pl

This is all working with the modifications.  I suspect our recent mass IT shut down may have had some side effects (i.e. stuff was upgraded quietly).

Must say the page seems to be much faster to render and open the different control panels.


With respect to the Bio::Graphics::FeatureFile error, what do you get when you run this from the command line:

   perl -MBio::Graphics::FeatureFile -e 0

This gives nothing when I use /usr/bin/perl (which is what GBrowse runs under and all installs are executed with, and a prefix location).


What does running this script give you:

 #!/usr/bin/perl
 use strict;
 use warnings;

 print Foo->new;
 exit 0;

 package Foo;
 use base 'Bio::Graphics::FeatureFile';
 sub new {
    my $class = shift;
    warn $class,': new()';
    return $class->SUPER::new(@_);
 }

cgp-gbrowse-test[kr2]192: /usr/bin/perl test.pl
Foo: new() at test.pl line 12.
Foo=HASH(0x1132190)



-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

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Re: GBrowse 2.20 released

Lincoln Stein-2
Hi Keiran,


On Thu, Jan 20, 2011 at 2:16 PM, Keiran Raine <[hidden email]> wrote:
On 20 Jan 2011, at 18:55, Lincoln Stein wrote:

There are two files that need modification: Filesystem.pm, and bin/gbrowse_metadb_config.pl

This is all working with the modifications.  I suspect our recent mass IT shut down may have had some side effects (i.e. stuff was upgraded quietly).

Are all tests running now? Did the "empty base class" error go away?

 

Must say the page seems to be much faster to render and open the different control panels.

Glad to hear it! The students and I did lots of work to improve performance. Have you tried turning on the details multiplier to get fast track panning?
 
With respect to the Bio::Graphics::FeatureFile error, what do you get when you run this from the command line:

   perl -MBio::Graphics::FeatureFile -e 0

This gives nothing when I use /usr/bin/perl (which is what GBrowse runs under and all installs are executed with, and a prefix location).


What does running this script give you:

 #!/usr/bin/perl
 use strict;
 use warnings;

 print Foo->new;
 exit 0;

 package Foo;
 use base 'Bio::Graphics::FeatureFile';
 sub new {
    my $class = shift;
    warn $class,': new()';
    return $class->SUPER::new(@_);
 }

cgp-gbrowse-test[kr2]192: /usr/bin/perl test.pl
Foo: new() at test.pl line 12.
Foo=HASH(0x1132190)

These are the expected results.

Lincoln 


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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