Hello, I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify "b258de1e6cea" version with hg clone command ? The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version. Thanks a lot, Sarah Maman
Hi Sarah, You should be able to do this with the -r option of the clone command, so: `hg clone -r b258de1e6cea https://bitbucket.org/galaxy/galaxy-dist`. -Dannon On Apr 25, 2012, at 3:08 AM, Sarah Maman wrote:
Hello,
I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify "b258de1e6cea" version with hg clone command ?
The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version.
Thanks a lot, Sarah Maman
From: Sarah Maman <sarah.maman@toulouse.inra.fr> Subject: Galaxy version Date: April 24, 2012 10:23:01 AM EDT To: Nate Coraor <nate@bx.psu.edu>, galaxy-dev-request@lists.bx.psu.edu
Hello,
I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify "b258de1e6cea" version with hg clone command ?
The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version.
Thanks a lot, Sarah Maman
___________________________________________________________ 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:
Thank you very much Dannon, it works. The more I discover Galaxy, the more I appreciate its use. Again, thank Galaxy team for this great tool. Sarah Maman Dannon Baker a écrit :
Hi Sarah,
You should be able to do this with the -r option of the clone command, so: `hg clone -r b258de1e6cea https://bitbucket.org/galaxy/galaxy-dist`.
-Dannon
On Apr 25, 2012, at 3:08 AM, Sarah Maman wrote:
Hello,
I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify "b258de1e6cea" version with hg clone command ?
The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version.
Thanks a lot, Sarah Maman
From: Sarah Maman <sarah.maman@toulouse.inra.fr> Subject: Galaxy version Date: April 24, 2012 10:23:01 AM EDT To: Nate Coraor <nate@bx.psu.edu>, galaxy-dev-request@lists.bx.psu.edu
Hello,
I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify "b258de1e6cea" version with hg clone command ?
The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version.
Thanks a lot, Sarah Maman
___________________________________________________________ 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:
Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, "Visualization" menu is absent and I think it should be related to the previous warning? How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote:
Hello,
After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning:
/WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/
Hi Sarah, I'm guessing that you are using a cluster with Galaxy. If this is correct, please try the following: 1. Log in to a cluster node as the user that runs Galaxy 2. cd to the galaxy-dist directory 3. run `python ./scripts/fetch_eggs.py` This should grab any missing eggs.
In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, "Visualization" menu is absent and I think it should be related to the previous warning?
See the 'enable_tracks' setting in universe_wsgi.ini to enable the Visualization menu. --nate
How to ensure that eggs be properly fetched?
Thank you in advance, Sarah Maman ___________________________________________________________ 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:
Thank Nate for your help. Visualization menu is now effective. However, I still have the problem of updating eggs. Indeed, galaxy is installed on a virtual machine and jobs run on SGE cluster. But I have been discouraged by my system administrator to run fetch_eggs.py scripts from our cluster node. If I run `python ./scripts/fetch_eggs.py` in galaxy-dist directory, as Galaxy user, but on my virtual machine, missing eggs are not grabed. Do you have another solution? Thanks, Sarah Nate Coraor a écrit :
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote:
Hello,
After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning:
/WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/
Hi Sarah,
I'm guessing that you are using a cluster with Galaxy. If this is correct, please try the following:
1. Log in to a cluster node as the user that runs Galaxy 2. cd to the galaxy-dist directory 3. run `python ./scripts/fetch_eggs.py`
This should grab any missing eggs.
In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, "Visualization" menu is absent and I think it should be related to the previous warning?
See the 'enable_tracks' setting in universe_wsgi.ini to enable the Visualization menu.
--nate
How to ensure that eggs be properly fetched?
Thank you in advance, Sarah Maman ___________________________________________________________ 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:
Hello, To solve this warning, python used by Galaxy is now localized on our server. I no longer use python available on our cluster. Thus, if python version on the cluster evolves, it will not impact Galaxy. Thanks to this modification, your script fetch_eggs.py have been start and some eggs have been updated except for Markupsafe. So I downloaded Markupsafe from Python website. Since then I have no warning on my runs ;-) Thanks, Sarah Nate Coraor a écrit :
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote:
Hello,
After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning:
/WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/
Hi Sarah,
I'm guessing that you are using a cluster with Galaxy. If this is correct, please try the following:
1. Log in to a cluster node as the user that runs Galaxy 2. cd to the galaxy-dist directory 3. run `python ./scripts/fetch_eggs.py`
This should grab any missing eggs.
In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, "Visualization" menu is absent and I think it should be related to the previous warning?
See the 'enable_tracks' setting in universe_wsgi.ini to enable the Visualization menu.
--nate
How to ensure that eggs be properly fetched?
Thank you in advance, Sarah Maman ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Dannon Baker -
Nate Coraor -
Sarah Maman