install_tool_shed_tools.py about ansible-galaxy-tools HOT 15 CLOSED

Thanks very much for all your help!!

Best,
Alberto

Il giorno 21 nov 2016, alle ore 16:58, Marius van den Beek [email protected] ha scritto:

You can find this here: https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/tool_list.yaml https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/tool_list.yaml
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https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/shed_install.py

The recommended way to use this is to do pip install ephemeris and then shed-install <your options>.

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Thanks,

from the Galaxy Web site I found instructions to use Ansible with https://github.com/afgane/galaxy-tools-playbook.git, but for my installation it does not work.
So I was looking around and I found some tutorials using install_tool_shed_tools.py.

Is then ephemeris the right tool to use in order to install tools in galaxy?

Best
Alberto

Il giorno 21 nov 2016, alle ore 12:54, Marius van den Beek [email protected] ha scritto:

https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/shed_install.py https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/shed_install.py
The recommended way to use this is to do pip install ephemeris and then shed-install .

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If you're not familiar with ansible, I would say yes, this is easier to setup and test.
This role makes use of ephemeris internally, so if your tool_list.yml file is fine, it should work both with this role and ephemeris.

I haven't had a chance to test this yet, but https://github.com/pjbriggs/nebulizer#managing-tools also looks like it's a great and easy way to install tools into galaxy.

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Well, I am new to galaxy installation and I am starting now making practices on Linux administration (Apache, MySQL and such common stuff). Ansible is new for me. So thanks a lot for your help, I hope to get galaxy tools installed :-)

Best,
Alberto

Il giorno 21 nov 2016, alle ore 13:11, Marius van den Beek [email protected] ha scritto:

If you're not familiar with ansible, I would say yes, this is easier to setup and test.
This role makes use of ephemeris internally, so if your tool_list.yml file is fine, it should work both with this role and ephemeris.

I haven't had a chance to test this yet, but https://github.com/pjbriggs/nebulizer#managing-tools also looks like it's a great and easy way to install tools into galaxy.

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Hello Marius,

I try a lot of times but I got a strange error.

shed-install --galaxy http://127.0.0.1:8080 --apikey 483f8c5f5e635acd701f19c5a7f1f653 --toolsfile tool_list.yaml;

with tool_list.yaml content:

tools:

• name: 'bowtie2'
  owner: 'devteam'
  tool_panel_section_label: 'My section'

If you would like to help me, I thank you very much!

Traceback (most recent call last):
File "/usr/local/bin/python2.7.12/bin/shed-install", line 11, in
sys.exit(script_main())
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/ephemeris/shed_install.py", line 720, in script_main
itm.install_tools()
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/ephemeris/shed_install.py", line 592, in install_tools
itl = installed_tool_revisions(self.gi) # installed tools list
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/ephemeris/shed_install.py", line 219, in installed_tool_revisions
itl = tsc.get_repositories()
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/bioblend/galaxy/toolshed/init.py", line 36, in get_repositories
return Client._get(self)
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/bioblend/galaxy/client.py", line 132, in _get
raise ConnectionError(msg, body=r.text,
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/requests/models.py", line 796, in text
if not self.content:
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/requests/models.py", line 772, in content
self._content = bytes().join(self.iter_content(CONTENT_CHUNK_SIZE)) or bytes()
File "/usr/local/bin/python2.7.12/lib/python2.7/site-packages/requests/models.py", line 705, in generate
chunk = self.raw.read(chunk_size)
AttributeError: 'NoneType' object has no attribute 'read'

Il giorno 21 nov 2016, alle ore 13:11, Marius van den Beek [email protected] ha scritto:

If you're not familiar with ansible, I would say yes, this is easier to setup and test.
This role makes use of ephemeris internally, so if your tool_list.yml file is fine, it should work both with this role and ephemeris.

I haven't had a chance to test this yet, but https://github.com/pjbriggs/nebulizer#managing-tools https://github.com/pjbriggs/nebulizer#managing-tools also looks like it's a great and easy way to install tools into galaxy.

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You're having trouble listing the installed repositories on your server,
which is the first interaction with galaxy in the script.
Could you try including a terminal /, so that the command reads

shed-install --galaxy http://127.0.0.1:8080/ --apikey 483f8c5f5e635acd701f19c5a7f1f653 --toolsfile tool_list.yaml

If that doesn't work, which version of galaxy are you using?

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Thanks,

no it is not working with shed-install --galaxy http://127.0.0.1:8080/ --apikey 483f8c5f5e635acd701f19c5a7f1f653 --toolsfile tool_list.yaml

In the meantime I tried unsuccessfully shed-install--galaxy http://127.0.0.1:8080 --apikey 483f8c5f5e635acd701f19c5a7f1f653 --name bowtie2 --owner devteam --section mysect --section_label mylab --toolshed https://toolshed.g2.bx.psu.edu

My Galaxy comes from git clone -b release_16.07 https://github.com/galaxyproject/galaxy.git;

The API key is associated with the Admin user. I do not installed Ansible, is it correct?
I am running on an Amazon EC2 virtual machine with Red Hat Enterprise Linux Server 7.3

Il giorno 21 nov 2016, alle ore 16:32, Marius van den Beek [email protected] ha scritto:

shed-install --galaxy http://127.0.0.1:8080/ http://127.0.0.1:8080/ --apikey 483f8c5f5e635acd701f19c5a7f1f653 --toolsfile tool_list.yaml

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I see now that galaxy/config folder does not contains a tool_sheds_conf.xml file, but tool_sheds_conf.xml.sample instead, I don’t know if this is correct

Il giorno 21 nov 2016, alle ore 16:32, Marius van den Beek [email protected] ha scritto:

shed-install --galaxy http://127.0.0.1:8080/ http://127.0.0.1:8080/ --apikey 483f8c5f5e635acd701f19c5a7f1f653 --toolsfile tool_list.yaml

from ansible-galaxy-tools.

I see now that galaxy/config folder does not contains a tool_sheds_conf.xml file, but tool_sheds_conf.xml.sample instead, I don’t know if this is correct

if you're just running galaxy with run.sh this is OK.

The API key is associated with the Admin user. I do not installed Ansible, is it correct?
I am running on an Amazon EC2 virtual machine with Red Hat Enterprise Linux Server 7.3

This is all OK.

Can you install tools manually through galaxy's UI?

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yes all ok now, see screenshot, a reboot solved all, I don’t understand why, but I am happy :)

did you known where I can obtain a yaml file with the tools installed in use usegalaxy.org?
my group would like to have a sort of local mirror

Il giorno 21 nov 2016, alle ore 16:51, Marius van den Beek [email protected] ha scritto:

I see now that galaxy/config folder does not contains a tool_sheds_conf.xml file, but tool_sheds_conf.xml.sample instead, I don’t know if this is correct

if you're just running galaxy with run.sh this is OK.

The API key is associated with the Admin user. I do not installed Ansible, is it correct?
I am running on an Amazon EC2 virtual machine with Red Hat Enterprise Linux Server 7.3

This is all OK.

Can you install tools manually through galaxy's UI?

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You can find this here: https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/tool_list.yaml

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I'm gonna close the issue, if you have more problems don't hesitate to open a new issue.

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Re. the file with the list of tools, the one linked higher up is a bit dated at this point. This file is a bit more recent although still no 100% match: https://github.com/galaxyproject/galaxy-cloudman-playbook/blob/master/files/usegalaxy_main_tool_list.yaml

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Thanks, I try it now

Il giorno 21 nov 2016, alle ore 17:06, Enis Afgan [email protected] ha scritto:

Re. the file with the list of tools, the one linked higher up is a bit dated at this point. This file is a bit more recent although still no 100% match: https://github.com/galaxyproject/galaxy-cloudman-playbook/blob/master/files/usegalaxy_main_tool_list.yaml https://github.com/galaxyproject/galaxy-cloudman-playbook/blob/master/files/usegalaxy_main_tool_list.yaml
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