Closed atermanini closed 7 years ago
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>
.
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 notifications@github.com 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.
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 notifications@github.com 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:
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
Il giorno 21 nov 2016, alle ore 13:11, Marius van den Beek notifications@github.com 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.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/galaxyproject/ansible-galaxy-tools/issues/38#issuecomment-261920812, or mute the thread https://github.com/notifications/unsubscribe-auth/ASXJkR4brlyV676q7HQKnEoIRGQ7ZCsIks5rAYqNgaJpZM4K4G2O.
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?
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 notifications@github.com ha scritto:
shed-install --galaxy http://127.0.0.1:8080/ http://127.0.0.1:8080/ --apikey 483f8c5f5e635acd701f19c5a7f1f653 --toolsfile tool_list.yaml
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 notifications@github.com ha scritto:
shed-install --galaxy http://127.0.0.1:8080/ http://127.0.0.1:8080/ --apikey 483f8c5f5e635acd701f19c5a7f1f653 --toolsfile tool_list.yaml
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?
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 notifications@github.com 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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Thanks very much for all your help!!
Best, Alberto
Il giorno 21 nov 2016, alle ore 16:58, Marius van den Beek notifications@github.com 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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/galaxyproject/ansible-galaxy-tools/issues/38#issuecomment-261978924, or mute the thread https://github.com/notifications/unsubscribe-auth/ASXJkVgx6b82AmENlQKi22VXf4kETRk2ks5rAb-SgaJpZM4K4G2O.
I'm gonna close the issue, if you have more problems don't hesitate to open a new issue.
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
Thanks, I try it now
Il giorno 21 nov 2016, alle ore 17:06, Enis Afgan notifications@github.com 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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/galaxyproject/ansible-galaxy-tools/issues/38#issuecomment-261981595, or mute the thread https://github.com/notifications/unsubscribe-auth/ASXJkcPtjNFDZdg0DR6LrqOntUMaja_nks5rAcGTgaJpZM4K4G2O.
where is this file now?