Hello Hakeem,
Did you ever solve this import problem?
We suddenly started seeing this on our main (old) Galaxy server,
which we have not intentionally changed recently:
$ hg log | head
changeset: 17125:e837a68e8d14
tag: tip
parent: 17121:7a4e3a661a76
parent: 17124:46a4ef8850
I haven't seen this before but did a little googling. What version is your
ansible installation? If it's a little bit older, (
https://github.com/ansible/ansible/issues/5412) might be what you're seeing.
It's a bit of a long read, but it looks like reinstalling or updating your
ansible (or inst
Hi Gildas, thanks for the reply.
I had renamed galaxy.ini.sample file to galaxy.ini and performed my
configurations to the server.
In fact, I created the file galaxy.ini.sample and command works fine!
Thanks a lot!
Best regards,
On Thu, Mar 3, 2016 at 5:46 AM Gildas Le Corguillé <
lecorgui...@sb
Hi everyone,
When I try to run galaxy using python 2.7 I get this error message while
fetching eggs. Under python 2.6 I do not have that issue:
DistributionNotFound: six==1.9.0
The galaxy release I use is still 15.07.
Is there any fix for that other than building the egg myself, or
Hi Bill,
I think you're trying to use the ansible-galaxy-tools role as a playbook:
This won't work, you can only include the role in your playbook,
or use this playbook https://github.com/afgane/galaxy-tools-playbook
You can also directly use the python script in
https://github.com/galaxyproject/a
Thanks Peter,
I heard support for 2.6 will be dropped, that is why I was investigating using
2.7 right now.
I will try to stage an update to 16.01 then and see how that works!
>From eggs to wheel, that's one big step in evolution :) haha
Yves Gagnon
-Original Message-
From: Peter Cock
On Fri, Mar 4, 2016 at 3:13 PM, Yves Gagnon wrote:
> Hi everyone,
>
> When I try to run galaxy using python 2.7 I get this error message while
> fetching eggs. Under python 2.6 I do not have that issue:
>
> DistributionNotFound: six==1.9.0
>
> The galaxy release I use is still 15.07.
>
> Is there
Hi all,
I know this is not a technical question per se, but this seems my best
option for getting better information.
I am planning on attending the Galaxy Conference this year. I administrate
the Galaxy server for VectorBase (vectorbase.org), but I'm a computer
scientist, not a bioinformatics sp
Hello Scott,
have you seen the schedule at https://gcc16.sched.org/ ?
The trainings are all listed, described, and categorized there, it should
help you decide what to attend.
>From my experience in addition to scientists there are many admins and
developers attending the conference so you should
Hi Martin,
Thank you for the quick response! However, I'm unclear... is "Training Day
One" different from the mix of individual session listed there, or does
training day one consist of those other sessions that I sign up for? I have
created a sched account, I'm just a bit confused about the relat
Hi Scott,
To my understanding the trainings (26th and 27th) comprise of the items
listed on the sched site. The Item you mentioned seems like a remnant of
how the sched site is organised and I would ignore it.
Someone will surely correct me if I am wrong.
Best,
M.
On Fri, Mar 4, 2016 at 11:48
On Thu, Mar 3, 2016 at 3:24 AM, Linda Bakker wrote:
> Hi Guys,
> So i updated my galaxy instance to release_16.01
> I usually started galaxy in a venv and used pip to install any packages my
> tool needed. (in this case, numpy and scipy)
>
> source my_galaxy_dir/.venv/bin/activate
> pip install s
On Thu, Mar 3, 2016 at 10:20 AM, Briand, Sheldon (NRC/CNRC) <
sheldon.bri...@canada.ca> wrote:
> Hi,
>
>
>
> I’ve done the recently announced security update for my running release
> which is 15.01. I figured I had better switch to git now while I was at
> it. However I’m having trouble matching
On Thu, Mar 3, 2016 at 1:09 PM, Ryan G wrote:
> Hi Nate - Thanks. Our galaxy.ini shows:
>
> job_config_file = config/job_conf.xml
>
> Our job_conf.xml is (which is the same as job_conf.xml.sample_basic) :
>
>
>
>
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
>
Thank you both, Marius and Dannon!
Since I am not familiar with ansible, I will just run the python script. I am
reading about the usage of the script, trying to figure out what configuration
needs to be in place and what options to use. Is there a step-by-step guide
for using this script som
There is no real step by step guide, but the script itself has a help text:
$ python install_tool_shed_tools.py -h
Also make sure you have bioblend installed (pip install bioblend)
It does more things than just installing tools. To just install tools you
would use a command line like this:
pyth
The list of tools installed on usegalaxy.org is conviniently desposited
here:
https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/tool_list.yaml
Normally you should be able to use this command outlined above to get all
the tools that usegalaxy.org has,
includ
Thanks a lot, Marius!
I am a newbie to this complex system and want a quick clone/install locally. I
have spent over two weeks on the process. There are many configuration files
and environment variables or dependencies to sort out. I wish the sample
configuration files would include most of th
Hi,
I posted this question to biostars but didn't get an answer
Is it possible to use "planemo test" functionality on an SGE cluster? I can
correctly run a custom tool on an SGE cluster when I manually run a job
through the galaxy interface. If I change the job_conf.xml so that the job
is run
On 4 March 2016 at 20:47, William Ge wrote:
> Thanks a lot, Marius!
>
> Sure, you're welcome!
> I am a newbie to this complex system and want a quick clone/install
> locally. I have spent over two weeks on the process. There are many
> configuration files and environment variables or dependenci
From: Marius van den Beek
Sent: Friday, March 4, 2016 12:26 PM
To: William Ge
Cc: Dannon Baker; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play
Thanks, Marius! That got me through!
The Galaxy Te
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