Yeah Linda, this was the case for me. When I started the virtual environment I
reinstalled BioPython and everything worked again. I suggest you do the same to
any packages you need for your tools.
Makis
To: galaxy-dev@lists.galaxyproject.org
From: linda.bak...@wur.nl
Date: Thu, 3 Mar 2016 14:10
Hi, all,
Sorry to bother you again. I am trying to install tools using the script. I
have downloaded the playbook, but stuck here:
[galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml -i
"localhost," --extra-vars galaxy_tools_api_key=xcd2Glx
ERROR: pip is not a legal parame
It worked! Thank you very much, Bjoern!
However, another error came up during the next step:
[galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml -i
"localhost," --extra-vars galaxy_tools_api_key=xcd2Glx
ERROR: pip is not a legal parameter of an Ansible Play
I did not find any
Hi,
try git clone --recursive
https://github.com/galaxyproject/ansible-galaxy-tools.git
Cheers,
Bjoern
Am 03.03.2016 um 19:54 schrieb William Ge:
> Hi, all,
>
>
>
> I tried to download the playbook for automatic installation of Galaxy
> tools, but encountered the following error:
>
>
>
>
Hi, all,
I tried to download the playbook for automatic installation of Galaxy tools,
but encountered the following error:
[galaxy@Pegasus galaxy]$ git clone --recursive
g...@github.com:afgane/galaxy-tools-playbook.git
Initialized empty Git repository in
/home/galaxy/galaxy/galaxy-tools-playbo
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) :
Hmmm, ok weird. We just restart Galaxy for the 5th or 6th time to get a
clean log fi
Hi John
Yes, I have do that :
>ls lib/galaxy/tools/toolbox/filters/examples.py*
lib/galaxy/tools/toolbox/filters/examples.py
lib/galaxy/tools/toolbox/filters/examples.py.sample
I'm currently trying to set up another galaxy server, I will try Galaxy 16.01
with this functionality.
Thank you fo
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 revisions in git.
I have looked at the instructions in the Develop/SourceCode page of the Wiki.
I've us
I guess this relates directly to my question as well...
On 03/03/2016 01:06 PM, Makis Ladoukakis wrote:
Hello everyone,
I've recently upgraded to Galaxy 16.01 and i have some issues with a
python wrapper from a tool. When I run it via Galaxy I get the
following error:
Traceback (most rece
On Thu, Mar 3, 2016 at 12:06 PM, Makis Ladoukakis
wrote:
> Hello everyone,
>
> I've recently upgraded to Galaxy 16.01 and i have some issues with a python
> wrapper from a tool. When I run it via Galaxy I get the following error:
>
> Traceback (most recent call last):
> File "/home/galaxy_user/g
Hello everyone,
I've recently upgraded to Galaxy 16.01 and i have some issues with a python
wrapper from a tool. When I run it via Galaxy I get the following error:
Traceback (most recent call last):
File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py",
line 12, in
fr
On Thu, Mar 3, 2016 at 9:14 AM, Peter Cock wrote:
> On Thu, Mar 3, 2016 at 8:24 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)
>>
On Thu, Mar 3, 2016 at 8:24 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)
>
> ...
>
> (.venv)@server:/galaxy-dist$ ./run.sh
> Activati
Hi,
Do you still have the config/galaxy.ini.sample file unchanged ?
We observed this message when some .sample are missing or were modified.
Gildas
-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateform ABiMS (Analyses and
Hi John,
thanks for your answer. The nginx config can be found at
https://gist.github.com/jenzopr/623c3541419ce33f662c
What I did was the following:
1) Stopping both servers, nginx and galaxy
2) Removing all log files and the tmp files in upload_store
3) Restarting the servers
4) Starting a fresh
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 scipy (dependency numpy also installed)
./run.sh
But since the l
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