Re: [galaxy-dev] Galaxy 16.01 Release

2016-02-25 Thread Makis Ladoukakis 
Thanks a lot Nate! You are right!

yum install mariadb-devel

did the trick.

Cheers,
Makis

From: n...@bx.psu.edu
Date: Thu, 25 Feb 2016 10:12:51 -0500
Subject: Re: [galaxy-dev] Galaxy 16.01 Release
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

On Thu, Feb 25, 2016 at 2:49 AM, Makis Ladoukakis  
wrote:



Just upgraded from the last version and after I run the run.sh script I get the 
following error:

mysql_config: command not found
Traceback (most recent call last):
  File "", line 1, in 
  File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in 
metadata, options = get_config()
  File "setup_posix.py", line 43, in get_config
libs = mysql_config("libs_r")
  File "setup_posix.py", line 25, in mysql_config
raise EnvironmentError("%s not found" % (mysql_config.path,))
EnvironmentError: mysql_config not found



Any idea why? 

I am running on CentOS 7.1.1503  with MariaDB installed.

Hi Makis,
Please make sure that you have the -devel package for MariaDB installed. 
MySQL_Python is looking for the `mysql_config` command to be able to build, but 
it's not present on your system.
--nate 

Kind regards,
Makis

From: n...@bx.psu.edu
Date: Wed, 24 Feb 2016 16:56:19 -0500
To: galaxy-annou...@lists.galaxyproject.org; galaxy-dev@lists.galaxyproject.org
CC: galaxy-committ...@lists.galaxyproject.org
Subject: [galaxy-dev] Galaxy 16.01 Release

The Galaxy Committers team is pleased to announce the January 2016 (v16.01) 
release of Galaxy. Galaxy administrators should also be aware of the security 
announcements that I am posting simultaneously with this release announcement. 
The release notes follow.

From: https://docs.galaxyproject.org/en/master/releases/16.01_announce.html


January 2016 Galaxy Release (v 16.01)
Highlights
Interactive Tours
The interactive tours framework allows developers and deployers to build 
interactive tutorials for users superimposed on the actual Galaxy web front 
end. Unlike video tutorials, these will not become stale and are truly 
interactive (allowing users to actually navigate and interact with Galaxy). 
Galaxy 16.01 ships with two example tours and new ones can easily be added by 
creating a small YAML file describing the tour. Try the Galaxy UI tour on Main.
Wheels
Galaxy’s Python dependencies have traditionally been distributed as eggs using 
custom dependency management code to enable Galaxy to distribute binary 
dependencies (enabling quick downloads and minimal system requirements). With 
this release all of that infrastructure has been replaced with a modern Python 
infrastructure based on pip and wheels. Work done as part of this to enable 
binary dependencies on Linux has been included with the recently released pip 8.
Detailed documentation on these changes and their impact under a variety of 
Galaxy deployment scenarios can be found in the Galaxy Framework Dependencies 
section of the Admin documentation.
Nested Workflows
Workflows may now run other workflows as a single abstract step in the parent 
workflow. This allows for reusing or subworkflows in your analyses.
Github
New% git clone -b master https://github.com/galaxyproject/galaxy.gitUpdate to 
latest stable release% git checkout master && pull --ff-only origin 
masterUpdate to exact version% git checkout v16.01
BitBucket
Upgrade% hg pull% hg update latest_16.01
See our wiki for additional details regarding the source code locations.
Deprecation Notices
Barring a strong outcry from deployers, 16.01 will be the last release of 
Galaxy to support Python 2.6. For more information, see Galaxy Github Issue 
#1596.

___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/ 
  

  ___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Galaxy 16.01 Release

2016-02-25 Thread Nate Coraor 
On Thu, Feb 25, 2016 at 2:49 AM, Makis Ladoukakis 
wrote:

> Just upgraded from the last version and after I run the run.sh script I
> get the following error:
>
> mysql_config: command not found
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in
> 
> metadata, options = get_config()
>   File "setup_posix.py", line 43, in get_config
> libs = mysql_config("libs_r")
>   File "setup_posix.py", line 25, in mysql_config
> raise EnvironmentError("%s not found" % (mysql_config.path,))
> EnvironmentError: mysql_config not found
>
>
>
> Any idea why?
>
> I am running on CentOS 7.1.1503  with MariaDB installed.
>

Hi Makis,

Please make sure that you have the -devel package for MariaDB installed.
MySQL_Python is looking for the `mysql_config` command to be able to build,
but it's not present on your system.

--nate


>
>
> Kind regards,
> Makis
>
> --
> From: n...@bx.psu.edu
> Date: Wed, 24 Feb 2016 16:56:19 -0500
> To: galaxy-annou...@lists.galaxyproject.org;
> galaxy-dev@lists.galaxyproject.org
> CC: galaxy-committ...@lists.galaxyproject.org
> Subject: [galaxy-dev] Galaxy 16.01 Release
>
>
> The Galaxy Committers team is pleased to announce the January 2016
> (v16.01) release of Galaxy. Galaxy administrators should also be aware of
> the security announcements that I am posting simultaneously with this
> release announcement. The release notes follow.
>
>
> From:
> https://docs.galaxyproject.org/en/master/releases/16.01_announce.html
>
>
> January 2016 Galaxy Release (v 16.01)
>
> Highlights
>
> *Interactive Tours*
>
> The interactive tours framework allows developers and deployers to build
> interactive tutorials for users superimposed on the actual Galaxy web front
> end. Unlike video tutorials, these will not become stale and are truly
> interactive (allowing users to actually navigate and interact with Galaxy).
> Galaxy 16.01 ships with two example tours and new ones can easily be added
> by creating a small YAML file describing the tour. Try the Galaxy UI tour
> on Main.
>
> *Wheels*
>
> Galaxy’s Python dependencies have traditionally been distributed as eggs
> using custom dependency management code to enable Galaxy to distribute
> binary dependencies (enabling quick downloads and minimal system
> requirements). With this release all of that infrastructure has been
> replaced with a modern Python infrastructure based on pip and wheels. Work
> done as part of this to enable binary dependencies on Linux has been
> included with the recently released pip 8.
>
> Detailed documentation on these changes and their impact under a variety
> of Galaxy deployment scenarios can be found in the Galaxy Framework
> Dependencies section of the Admin documentation.
>
> *Nested Workflows*
>
> Workflows may now run other workflows as a single abstract step in the
> parent workflow. This allows for reusing or subworkflows in your analyses.
>
> Github
>
> *New*
> % git clone -b master https://github.com/galaxyproject/galaxy.git
> *Update to latest stable release*
> % git checkout master && pull --ff-only origin master
> *Update to exact version*
> % git checkout v16.01
>
> BitBucket
>
> *Upgrade*
> % hg pull
> % hg update latest_16.01
>
> See our wiki for additional details regarding the source code locations.
>
> Deprecation Notices
>
> Barring a strong outcry from deployers, 16.01 will be the last release of
> Galaxy to support Python 2.6. For more information, see Galaxy Github Issue
> #1596.
>
> ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use
> the unified search at: http://galaxyproject.org/search/mailinglists/
>
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Galaxy 16.01 Release

2016-02-24 Thread Makis Ladoukakis 
Just upgraded from the last version and after I run the run.sh script I get the 
following error:

mysql_config: command not found
Traceback (most recent call last):
  File "", line 1, in 
  File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in 
metadata, options = get_config()
  File "setup_posix.py", line 43, in get_config
libs = mysql_config("libs_r")
  File "setup_posix.py", line 25, in mysql_config
raise EnvironmentError("%s not found" % (mysql_config.path,))
EnvironmentError: mysql_config not found



Any idea why? 

I am running on CentOS 7.1.1503  with MariaDB installed.


Kind regards,
Makis

From: n...@bx.psu.edu
Date: Wed, 24 Feb 2016 16:56:19 -0500
To: galaxy-annou...@lists.galaxyproject.org; galaxy-dev@lists.galaxyproject.org
CC: galaxy-committ...@lists.galaxyproject.org
Subject: [galaxy-dev] Galaxy 16.01 Release

The Galaxy Committers team is pleased to announce the January 2016 (v16.01) 
release of Galaxy. Galaxy administrators should also be aware of the security 
announcements that I am posting simultaneously with this release announcement. 
The release notes follow.

From: https://docs.galaxyproject.org/en/master/releases/16.01_announce.html


January 2016 Galaxy Release (v 16.01)
Highlights
Interactive Tours
The interactive tours framework allows developers and deployers to build 
interactive tutorials for users superimposed on the actual Galaxy web front 
end. Unlike video tutorials, these will not become stale and are truly 
interactive (allowing users to actually navigate and interact with Galaxy). 
Galaxy 16.01 ships with two example tours and new ones can easily be added by 
creating a small YAML file describing the tour. Try the Galaxy UI tour on Main.
Wheels
Galaxy’s Python dependencies have traditionally been distributed as eggs using 
custom dependency management code to enable Galaxy to distribute binary 
dependencies (enabling quick downloads and minimal system requirements). With 
this release all of that infrastructure has been replaced with a modern Python 
infrastructure based on pip and wheels. Work done as part of this to enable 
binary dependencies on Linux has been included with the recently released pip 8.
Detailed documentation on these changes and their impact under a variety of 
Galaxy deployment scenarios can be found in the Galaxy Framework Dependencies 
section of the Admin documentation.
Nested Workflows
Workflows may now run other workflows as a single abstract step in the parent 
workflow. This allows for reusing or subworkflows in your analyses.
Github
New% git clone -b master https://github.com/galaxyproject/galaxy.gitUpdate to 
latest stable release% git checkout master && pull --ff-only origin 
masterUpdate to exact version% git checkout v16.01
BitBucket
Upgrade% hg pull% hg update latest_16.01
See our wiki for additional details regarding the source code locations.
Deprecation Notices
Barring a strong outcry from deployers, 16.01 will be the last release of 
Galaxy to support Python 2.6. For more information, see Galaxy Github Issue 
#1596.

___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/ 
  ___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Galaxy 16.01 Release

2016-02-24 Thread Nate Coraor 
The Galaxy Committers team is pleased to announce the January 2016 (v16.01)
release of Galaxy. Galaxy administrators should also be aware of the
security announcements that I am posting simultaneously with this release
announcement. The release notes follow.


From: https://docs.galaxyproject.org/en/master/releases/16.01_announce.html


January 2016 Galaxy Release (v 16.01)

Highlights

*Interactive Tours*

The interactive tours framework allows developers and deployers to build
interactive tutorials for users superimposed on the actual Galaxy web front
end. Unlike video tutorials, these will not become stale and are truly
interactive (allowing users to actually navigate and interact with Galaxy).
Galaxy 16.01 ships with two example tours and new ones can easily be added
by creating a small YAML file describing the tour. Try the Galaxy UI tour
on Main.

*Wheels*

Galaxy’s Python dependencies have traditionally been distributed as eggs
using custom dependency management code to enable Galaxy to distribute
binary dependencies (enabling quick downloads and minimal system
requirements). With this release all of that infrastructure has been
replaced with a modern Python infrastructure based on pip and wheels. Work
done as part of this to enable binary dependencies on Linux has been
included with the recently released pip 8.

Detailed documentation on these changes and their impact under a variety of
Galaxy deployment scenarios can be found in the Galaxy Framework
Dependencies section of the Admin documentation.

*Nested Workflows*

Workflows may now run other workflows as a single abstract step in the
parent workflow. This allows for reusing or subworkflows in your analyses.

Github

*New*
% git clone -b master https://github.com/galaxyproject/galaxy.git
*Update to latest stable release*
% git checkout master && pull --ff-only origin master
*Update to exact version*
% git checkout v16.01

BitBucket

*Upgrade*
% hg pull
% hg update latest_16.01

See our wiki for additional details regarding the source code locations.

Deprecation Notices

Barring a strong outcry from deployers, 16.01 will be the last release of
Galaxy to support Python 2.6. For more information, see Galaxy Github Issue
#1596.
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/