Pablo Moreno

Which functions of MATLAB Cobra toolbox are available or not on cobrapy?

4

Hi there! Thanks for all the excellent work on cobrapy! Is there any reference/wiki page/comparison table that shows which functionality/methods on the Matlab version are available (or not) on the...

[compose] /export/venv should be part of galaxy-web and not galaxy-init

3

Starting the compose setup on virtualised file system can take easily 10 minutes, a lot in part due to the needed copies from the init container to the shared filesystem....

Hi there! We have a script on galaxyproject/galaxy-kubernetes for building the compose containers for kubernetes (they require certain env vars to be set, plus other ad-hoc flexibility): https://github.com/galaxyproject/galaxy-kubernetes/blob/develop/build-community-images-for-k8s.sh But it...

18.01 on Kubernetes fails lifting Galaxy due to missing galaxy.yml

5

Currently failing on k8s due to: ``` Waiting for database Traceback (most recent call last): File "/usr/local/bin/check_database.py", line 18, in db_url = get_config(sys.argv)['db_url'] File "/export/galaxy-central/lib/galaxy/model/orm/scripts.py", line 126, in get_config properties...

[18.01] [compose] Handler logs don't seem to make it to /home/galaxy/logs

1

Hi there! It seems to be that logs for the handlers are not making it for some reason to /home/galaxy/logs: ``` root@whimsical-monkey-galaxy-stable-7dbb6c4c6b-lcqsr:~/logs# pwd /home/galaxy/logs root@whimsical-monkey-galaxy-stable-7dbb6c4c6b-lcqsr:~/logs# ls -ltr total 268 -rw-r--r--...

[18.01] galaxy:galaxy_nodejs_proxy not starting due to `node` missing

1

On 18.01 I'm getting inside supervisorctl: ``` galaxy:galaxy_nodejs_proxy FATAL Exited too quickly (process log may have details) ``` Upon inspection: ``` supervisor> tail galaxy:galaxy_nodejs_proxy /usr/bin/env: node: No such file or...

[compose] If supervisor fails to lift Galaxy, the container should exit with an error

1

Currently in the compose setup, if galaxy fails to be lifted by supervisor, the latter keeps trying to lift it and the container never fails (as you would expect in...

[compose] Should galaxy postgres schema dump be stored with the postgres container?

1

I'm wondering whether the best place to store the sql dump of the galaxy database is the postgres container, being the main caveat that you could be using incompatible tags...

API documentation? How can I get data for specific dates for a sensor?

1

Hi! Thanks for this great project and datasource! I'm interested in data for particular dates and defined sensors and I see that you have an API. I want to get...

Support for /api/container_resolvers/toolbox/install method

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This PR adds the ability for the install_tool_dependency to use the container_resolvers resolver, so that singularity (and other containers) can be downloaded by Galaxy on request of this method. If...