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.
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 "<string>", line 1, in <module> File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in <module> 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: nate@bx.psu.edu Date: Wed, 24 Feb 2016 16:56:19 -0500 To: galaxy-announce@lists.galaxyproject.org; galaxy-dev@lists.galaxyproject.org CC: galaxy-committers@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/
On Thu, Feb 25, 2016 at 2:49 AM, Makis Ladoukakis <makis4ever@hotmail.com> 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 "<string>", line 1, in <module> File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in <module> 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: nate@bx.psu.edu Date: Wed, 24 Feb 2016 16:56:19 -0500 To: galaxy-announce@lists.galaxyproject.org; galaxy-dev@lists.galaxyproject.org CC: galaxy-committers@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/
Thanks a lot Nate! You are right! yum install mariadb-devel did the trick. Cheers, Makis From: nate@bx.psu.edu Date: Thu, 25 Feb 2016 10:12:51 -0500 Subject: Re: [galaxy-dev] Galaxy 16.01 Release To: makis4ever@hotmail.com CC: galaxy-dev@lists.galaxyproject.org On Thu, Feb 25, 2016 at 2:49 AM, Makis Ladoukakis <makis4ever@hotmail.com> 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 "<string>", line 1, in <module> File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in <module> 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: nate@bx.psu.edu Date: Wed, 24 Feb 2016 16:56:19 -0500 To: galaxy-announce@lists.galaxyproject.org; galaxy-dev@lists.galaxyproject.org CC: galaxy-committers@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/
participants (2)
-
Makis Ladoukakis -
Nate Coraor