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/ansible-galaxy-tools/blob/master/files/inst... if you're more comfortable not using ansible.

Cheers, Marius

On 4 March 2016 at 13:43, Dannon Baker dannon.baker@gmail.com wrote:

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 installing a new one in a fresh virtualenv for isolation) should resolve it.

Let me know if that doesn't fix it up for you.

On Thu, Mar 3, 2016 at 10:08 PM, William Ge wge@centrilliontech.com wrote:

...

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 parameter of an Ansible Play

I did not find anything related on the Galaxy search either. Any help will be appreciated.

The web Admin interface only allows tool installation one by one. I wish it allows batch installation there.

Thanks,

Bill

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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:

python install_tool_shed_tools.py -a "your new admin api key" -g "your new galaxy instance url" -t tool_list.yml

tool_list.yml follows the format outlined here: https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool...

Cheers, Marius ​

On 4 March 2016 at 19:11, William Ge wge@centrilliontech.com wrote:

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 somewhere?

Best regards, Bill

---

*From:* Marius van den Beek m.vandenbeek@gmail.com *Sent:* Friday, March 4, 2016 7:25 AM *To:* Dannon Baker *Cc:* William Ge; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

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 https://github.com/afgane/galaxy-tools-playbook afgane/galaxy-tools-playbook · GitHub https://github.com/afgane/galaxy-tools-playbook github.com README.md A ready-to-use Ansible playbook for the Galaxy Tools role. Before you can use this playbook, you need to install Ansible: $ pip install ansible You can also directly use the python script in https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/inst... if you're more comfortable not using ansible.

Cheers, Marius

On 4 March 2016 at 13:43, Dannon Baker dannon.baker@gmail.com wrote:

...

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 installing a new one in a fresh virtualenv for isolation) should resolve it.

Let me know if that doesn't fix it up for you.

On Thu, Mar 3, 2016 at 10:08 PM, William Ge wge@centrilliontech.com wrote:

...

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 parameter of an Ansible Play

I did not find anything related on the Galaxy search either. Any help will be appreciated.

The web Admin interface only allows tool installation one by one. I wish it allows batch installation there.

Thanks,

Bill

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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 the options so that new installation just needs to comment out or delete unwanted ones.

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

Thanks,

Bill

________________________________ From: Marius van den Beek m.vandenbeek@gmail.com Sent: Friday, March 4, 2016 11:03 AM 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

The list of tools installed on usegalaxy.orghttp://usegalaxy.org/ is conviniently desposited here: Galaxyhttp://usegalaxy.org/ usegalaxy.org The Galaxy analysis interface requires a browser with Javascript enabled. Please enable Javascript and refresh this page. Galaxy. Javascript Required for Galaxy

https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy...

Normally you should be able to use this command outlined above to get all the tools that usegalaxy.orghttp://usegalaxy.org/ has, including the dependencies.

PS. please keep all traffic on the mailing list

On 4 March 2016 at 19:59, Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com> wrote:

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:

python install_tool_shed_tools.py -a "your new admin api key" -g "your new galaxy instance url" -t tool_list.yml

tool_list.yml follows the format outlined here: https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool...

Cheers, Marius

On 4 March 2016 at 19:11, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote:

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 somewhere?

Best regards, Bill

________________________________ From: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com> Sent: Friday, March 4, 2016 7:25 AM To: Dannon Baker Cc: William Ge; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

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 [https://avatars0.githubusercontent.com/u/338642?v=3&s=400]https://github.com/afgane/galaxy-tools-playbook

afgane/galaxy-tools-playbook · GitHubhttps://github.com/afgane/galaxy-tools-playbook github.comhttp://github.com README.md A ready-to-use Ansible playbook for the Galaxy Tools role. Before you can use this playbook, you need to install Ansible: $ pip install ansible

You can also directly use the python script in https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/inst... if you're more comfortable not using ansible.

Cheers, Marius

On 4 March 2016 at 13:43, Dannon Baker <dannon.baker@gmail.commailto:dannon.baker@gmail.com> wrote: 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 installing a new one in a fresh virtualenv for isolation) should resolve it.

Let me know if that doesn't fix it up for you.

On Thu, Mar 3, 2016 at 10:08 PM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: 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 parameter of an Ansible Play

I did not find anything related on the Galaxy search either. Any help will be appreciated.

The web Admin interface only allows tool installation one by one. I wish it allows batch installation there.

Thanks,

Bill

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

________________________________ From: Marius van den Beek m.vandenbeek@gmail.com 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 Team has done a wonderful job putting together such a complex system. It is very well packaged and documented good enough for developers. But for new people like me, a more fool-proof step-by-step guide will be very helpful. I have worked with ACEDB, GCG, LionBioscience SRS and other early bioinformatics packages in the past, but have been out of touch for a while. The most challenging portion for me is to sort out the configuration files, retrieve/download data and install tools. The web admin application is a good tool. It would be very helpful for new people if there is a check box in front of the categories of tools, and in front of each individual tools, so that we can check to select and click install to perform batch install there.

Best regards, Bill

On 4 March 2016 at 20:47, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> 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 dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going. If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

This is indeed a python2.6 issue. Note that python2.6 has reached it's EOL in October 2013 (https://www.python.org/download/releases/2.6.9/), and python2.6 support for galaxy will be phased out with the next release (https://github.com/galaxyproject/galaxy/issues/1596), so it's probably a good idea to look into migrating to python2.7. That said, you can try this patch https://github.com/galaxyproject/ansible-galaxy-tools/compare/master...galax... In addition, there may be a bioblend problem in combination with recent galaxy releases. I'll let you know once this is sorted out.

Thanks,

Bill

________________________________ From: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com> Sent: Friday, March 4, 2016 11:03 AM To: William Ge Cc: Dannon Baker; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

The list of tools installed on usegalaxy.orghttp://usegalaxy.org/ is conviniently desposited here: Galaxyhttp://usegalaxy.org/ usegalaxy.orghttp://usegalaxy.org The Galaxy analysis interface requires a browser with Javascript enabled. Please enable Javascript and refresh this page. Galaxy. Javascript Required for Galaxy

https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy...

Normally you should be able to use this command outlined above to get all the tools that usegalaxy.orghttp://usegalaxy.org/ has, including the dependencies.

PS. please keep all traffic on the mailing list

On 4 March 2016 at 19:59, Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com> wrote:

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:

python install_tool_shed_tools.py -a "your new admin api key" -g "your new galaxy instance url" -t tool_list.yml

tool_list.yml follows the format outlined here: https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool...

Cheers, Marius

On 4 March 2016 at 19:11, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote:

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 somewhere?

Best regards, Bill

________________________________ From: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com> Sent: Friday, March 4, 2016 7:25 AM To: Dannon Baker Cc: William Ge; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

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 [https://avatars0.githubusercontent.com/u/338642?v=3&s=400]https://github.com/afgane/galaxy-tools-playbook

afgane/galaxy-tools-playbook · GitHubhttps://github.com/afgane/galaxy-tools-playbook github.comhttp://github.com README.md A ready-to-use Ansible playbook for the Galaxy Tools role. Before you can use this playbook, you need to install Ansible: $ pip install ansible

You can also directly use the python script in https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/inst... if you're more comfortable not using ansible.

Cheers, Marius

On 4 March 2016 at 13:43, Dannon Baker <dannon.baker@gmail.commailto:dannon.baker@gmail.com> wrote: 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 installing a new one in a fresh virtualenv for isolation) should resolve it.

Let me know if that doesn't fix it up for you.

On Thu, Mar 3, 2016 at 10:08 PM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: 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 parameter of an Ansible Play

I did not find anything related on the Galaxy search either. Any help will be appreciated.

The web Admin interface only allows tool installation one by one. I wish it allows batch installation there.

Thanks,

Bill

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hi Bill, Do you have the value set in Galaxy's *$GALAXY_ROOT/config/galaxy.ini* file for setting *tool_config_file *option? I believe this variable should be set to a file other than the default **.sample*.

On Wed, Apr 6, 2016 at 9:21 PM, William Ge wge@centrilliontech.com wrote:

Hi, Marius,

I got ansible running and installed the tools on my local instance of Galaxy. However, the tools are not shown on the tool panel on the web page. Wonder if the tools has been installed in the wrong place, or something else is wrong. Have been searching the Wiki and list without any resulst. Please point me to the right directions.

Thanks,

Bill

*From:* Marius van den Beek [mailto:m.vandenbeek@gmail.com] *Sent:* Friday, March 4, 2016 12:27 PM *To:* William Ge wge@centrilliontech.com *Cc:* Dannon Baker dannon.baker@gmail.com; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

On 4 March 2016 at 20:47, William Ge wge@centrilliontech.com 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 dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going.

If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

The location of that dir is defined in shed_tool_conf.xml[.sample] and defaults to ../shed_tools. The reasoning is described here, under item #2: https://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Tool_Shed

On Thu, Apr 7, 2016 at 11:09 AM, William Ge wge@centrilliontech.com wrote:

Thanks, Enis!

Yes, that line was uncommented with the option pointing to “tool_conf.xml,shed_tool_conf.xml”. However, I noticed that the “shed_tool_conf.xml” has not been changed after running the ansible-playbook to install tools. One other thing: the shed_tools directory was one level above the Galaxy subdirectories: i.e., all subdirectories (config, database, tool-data, tools, static, etc) are in /home/galaxy/galaxy, while “shed_tools” is in /home/galaxy. Do not know why.

Thanks,

Bill

*From:* Enis Afgan [mailto:enis.afgan@irb.hr] *Sent:* Thursday, April 7, 2016 7:06 AM *To:* William Ge wge@centrilliontech.com *Cc:* Marius van den Beek m.vandenbeek@gmail.com; galaxy-dev@lists.galaxyproject.org

*Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill,

Do you have the value set in Galaxy's *$GALAXY_ROOT/config/galaxy.ini* file for setting *tool_config_file *option? I believe this variable should be set to a file other than the default **.sample*.

On Wed, Apr 6, 2016 at 9:21 PM, William Ge wge@centrilliontech.com wrote:

Hi, Marius,

I got ansible running and installed the tools on my local instance of Galaxy. However, the tools are not shown on the tool panel on the web page. Wonder if the tools has been installed in the wrong place, or something else is wrong. Have been searching the Wiki and list without any resulst. Please point me to the right directions.

Thanks,

Bill

*From:* Marius van den Beek [mailto:m.vandenbeek@gmail.com] *Sent:* Friday, March 4, 2016 12:27 PM *To:* William Ge wge@centrilliontech.com *Cc:* Dannon Baker dannon.baker@gmail.com; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

On 4 March 2016 at 20:47, William Ge wge@centrilliontech.com 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 dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going.

If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Does anyone know why Ansible installation of the tools did not update the shed_tools_conf.xml file to reflect the installed tools? How can I make the tools installed with the Ansible playbook visible on the web front end? Thanks, Bill

From: Enis Afgan [mailto:enis.afgan@irb.hr] Sent: Friday, April 8, 2016 9:19 AM To: William Ge wge@centrilliontech.com Cc: Marius van den Beek m.vandenbeek@gmail.com; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

The location of that dir is defined in shed_tool_conf.xml[.sample] and defaults to ../shed_tools. The reasoning is described here, under item #2: https://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Tool_Shed

On Thu, Apr 7, 2016 at 11:09 AM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: Thanks, Enis! Yes, that line was uncommented with the option pointing to “tool_conf.xml,shed_tool_conf.xml”. However, I noticed that the “shed_tool_conf.xml” has not been changed after running the ansible-playbook to install tools. One other thing: the shed_tools directory was one level above the Galaxy subdirectories: i.e., all subdirectories (config, database, tool-data, tools, static, etc) are in /home/galaxy/galaxy, while “shed_tools” is in /home/galaxy. Do not know why.

Thanks, Bill

From: Enis Afgan [mailto:enis.afgan@irb.hrmailto:enis.afgan@irb.hr] Sent: Thursday, April 7, 2016 7:06 AM To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org

Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill, Do you have the value set in Galaxy's $GALAXY_ROOT/config/galaxy.ini file for setting tool_config_file option? I believe this variable should be set to a file other than the default *.sample.

On Wed, Apr 6, 2016 at 9:21 PM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote:

Hi, Marius,

I got ansible running and installed the tools on my local instance of Galaxy. However, the tools are not shown on the tool panel on the web page. Wonder if the tools has been installed in the wrong place, or something else is wrong. Have been searching the Wiki and list without any resulst. Please point me to the right directions.

Thanks,

Bill

From: Marius van den Beek [mailto:m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com] Sent: Friday, March 4, 2016 12:27 PM To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Dannon Baker <dannon.baker@gmail.commailto:dannon.baker@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

On 4 March 2016 at 20:47, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> 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 dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going.

If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Thanks, Marius!

Sure, here it is: I followed the online instructions to git clone the master Galaxy (Feb., 2016) and configured it for local production use with PostgreSQL and proftp. First tried ansible to install the tools, but did not succeed. Then tried the online admin installation of tools one-by-one. That worked, and I installed at least one tool for each section this way. With more help from you and others later, I got ansible-playbook to run to install the tools. That ran OK, but did not see the tools installed show up on the web frontend.

Beginning of the tool_list.yml is the same as the one included in the playbook/roles, except for the api_key and galaxy_instance:

api_key: ‘d22b682…’ galaxy_instance: 127.0.0.1:8080 tools:

- name: ‘column_maker’

owner: …

The command I used is: ansible-playbook tools.yaml The playbook was downloaded end of March, following the link given on the Galaxy tool installation guide. Manual installation of the tools one-by-one from the Admin web page works. The tools installed show up on the web page.

Thanks, Bill From: Marius van den Beek [mailto:m.vandenbeek@gmail.com] Sent: Thursday, April 21, 2016 9:45 AM To: William Ge wge@centrilliontech.com Cc: Enis Afgan enis.afgan@irb.hr; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill, can you describe what exactly you have done? What would be good is if you could post the beginning of your tool_list.yml file, the command that you used to run the playbook, the version of galaxy and the last commit of the playbook you are using (the last entry of `git log`). For any of this to work you should also be able manually install tools from the toolshed. Does this work for you?

On 21 April 2016 at 18:14, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: Does anyone know why Ansible installation of the tools did not update the shed_tools_conf.xml file to reflect the installed tools? How can I make the tools installed with the Ansible playbook visible on the web front end? Thanks, Bill

From: Enis Afgan [mailto:enis.afgan@irb.hrmailto:enis.afgan@irb.hr] Sent: Friday, April 8, 2016 9:19 AM

To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

The location of that dir is defined in shed_tool_conf.xml[.sample] and defaults to ../shed_tools. The reasoning is described here, under item #2: https://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Tool_Shed

On Thu, Apr 7, 2016 at 11:09 AM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: Thanks, Enis! Yes, that line was uncommented with the option pointing to “tool_conf.xml,shed_tool_conf.xml”. However, I noticed that the “shed_tool_conf.xml” has not been changed after running the ansible-playbook to install tools. One other thing: the shed_tools directory was one level above the Galaxy subdirectories: i.e., all subdirectories (config, database, tool-data, tools, static, etc) are in /home/galaxy/galaxy, while “shed_tools” is in /home/galaxy. Do not know why.

Thanks, Bill

From: Enis Afgan [mailto:enis.afgan@irb.hrmailto:enis.afgan@irb.hr] Sent: Thursday, April 7, 2016 7:06 AM To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org

Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill, Do you have the value set in Galaxy's $GALAXY_ROOT/config/galaxy.ini file for setting tool_config_file option? I believe this variable should be set to a file other than the default *.sample.

On Wed, Apr 6, 2016 at 9:21 PM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote:

Hi, Marius,

I got ansible running and installed the tools on my local instance of Galaxy. However, the tools are not shown on the tool panel on the web page. Wonder if the tools has been installed in the wrong place, or something else is wrong. Have been searching the Wiki and list without any resulst. Please point me to the right directions.

Thanks,

Bill

From: Marius van den Beek [mailto:m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com] Sent: Friday, March 4, 2016 12:27 PM To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Dannon Baker <dannon.baker@gmail.commailto:dannon.baker@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

On 4 March 2016 at 20:47, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> 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 dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going.

If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Oh, and one more thing, when you install the tools through the playbook, do they appear in the admin section?

On 21 April 2016 at 19:37, Marius van den Beek m.vandenbeek@gmail.com wrote:

Okay, that was a bit too short for the tool_list.yml. What is important is that you either have the tool_panel_section_label or tool_panel_section_id included in your tool_list.yml (for each tool!). Then it would help us to see what is going on if you can run the playbook with the -vvvv parameter, as well as what is going on at the same time in your galaxy logs.

On 21 April 2016 at 19:30, William Ge wge@centrilliontech.com wrote:

...

Thanks, Marius!

Sure, here it is:

I followed the online instructions to git clone the master Galaxy (Feb., 2016) and configured it for local production use with PostgreSQL and proftp. First tried ansible to install the tools, but did not succeed. Then tried the online admin installation of tools one-by-one. That worked, and I installed at least one tool for each section this way. With more help from you and others later, I got ansible-playbook to run to install the tools. That ran OK, but did not see the tools installed show up on the web frontend.

Beginning of the tool_list.yml is the same as the one included in the playbook/roles, except for the api_key and galaxy_instance:

api_key: ‘d22b682…’

galaxy_instance: 127.0.0.1:8080

tools:

•      name: ‘column_maker’
  
  

owner: …

The command I used is: ansible-playbook tools.yaml

The playbook was downloaded end of March, following the link given on the Galaxy tool installation guide.

Manual installation of the tools one-by-one from the Admin web page works. The tools installed show up on the web page.

Thanks,

Bill

*From:* Marius van den Beek [mailto:m.vandenbeek@gmail.com] *Sent:* Thursday, April 21, 2016 9:45 AM *To:* William Ge wge@centrilliontech.com *Cc:* Enis Afgan enis.afgan@irb.hr; galaxy-dev@lists.galaxyproject.org

*Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill, can you describe what exactly you have done?

What would be good is if you could post the beginning of your tool_list.yml file,

the command that you used to run the playbook, the version of galaxy and the last commit

of the playbook you are using (the last entry of `git log`).

For any of this to work you should also be able manually install tools from the toolshed.

Does this work for you?

On 21 April 2016 at 18:14, William Ge wge@centrilliontech.com wrote:

Does anyone know why Ansible installation of the tools did not update the shed_tools_conf.xml file to reflect the installed tools? How can I make the tools installed with the Ansible playbook visible on the web front end?

Thanks,

Bill

*From:* Enis Afgan [mailto:enis.afgan@irb.hr] *Sent:* Friday, April 8, 2016 9:19 AM

*To:* William Ge wge@centrilliontech.com *Cc:* Marius van den Beek m.vandenbeek@gmail.com; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

The location of that dir is defined in shed_tool_conf.xml[.sample] and defaults to ../shed_tools. The reasoning is described here, under item #2: https://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Tool_Shed

On Thu, Apr 7, 2016 at 11:09 AM, William Ge wge@centrilliontech.com wrote:

Thanks, Enis!

Yes, that line was uncommented with the option pointing to “tool_conf.xml,shed_tool_conf.xml”. However, I noticed that the “shed_tool_conf.xml” has not been changed after running the ansible-playbook to install tools. One other thing: the shed_tools directory was one level above the Galaxy subdirectories: i.e., all subdirectories (config, database, tool-data, tools, static, etc) are in /home/galaxy/galaxy, while “shed_tools” is in /home/galaxy. Do not know why.

Thanks,

Bill

*From:* Enis Afgan [mailto:enis.afgan@irb.hr] *Sent:* Thursday, April 7, 2016 7:06 AM *To:* William Ge wge@centrilliontech.com *Cc:* Marius van den Beek m.vandenbeek@gmail.com; galaxy-dev@lists.galaxyproject.org

*Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill,

Do you have the value set in Galaxy's *$GALAXY_ROOT/config/galaxy.ini* file for setting *tool_config_file *option? I believe this variable should be set to a file other than the default **.sample*.

On Wed, Apr 6, 2016 at 9:21 PM, William Ge wge@centrilliontech.com wrote:

Hi, Marius,

I got ansible running and installed the tools on my local instance of Galaxy. However, the tools are not shown on the tool panel on the web page. Wonder if the tools has been installed in the wrong place, or something else is wrong. Have been searching the Wiki and list without any resulst. Please point me to the right directions.

Thanks,

Bill

*From:* Marius van den Beek [mailto:m.vandenbeek@gmail.com] *Sent:* Friday, March 4, 2016 12:27 PM *To:* William Ge wge@centrilliontech.com *Cc:* Dannon Baker dannon.baker@gmail.com; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

On 4 March 2016 at 20:47, William Ge wge@centrilliontech.com 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 dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going.

If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Sorry, my previous message were held by the list moderator due to its size: I attached the logs and files. Anyway, here are my short answers: No, the tools do no show on the admin section Yes, the section id is included in the tool_list.yaml file. The file was downloaded along with the play-book. I only modified the key and host Ip The shed_tool_conf.xml was not modified after ansible-playbook ran. Is this file supposed to be modified by ansible to reflect the newly installed tools, and then incorporated into integrated_tool_conf.xml in order to show on the web page? Sorry the attachment did not get through. I will try to email you directly.

Thanks, Bill

From: Marius van den Beek [mailto:m.vandenbeek@gmail.com] Sent: Thursday, April 21, 2016 10:39 AM To: William Ge wge@centrilliontech.com Cc: Enis Afgan enis.afgan@irb.hr; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Oh, and one more thing, when you install the tools through the playbook, do they appear in the admin section?

On 21 April 2016 at 19:37, Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com> wrote: Okay, that was a bit too short for the tool_list.yml. What is important is that you either have the tool_panel_section_label or tool_panel_section_id included in your tool_list.yml (for each tool!). Then it would help us to see what is going on if you can run the playbook with the -vvvv parameter, as well as what is going on at the same time in your galaxy logs.

On 21 April 2016 at 19:30, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: Thanks, Marius!

Sure, here it is: I followed the online instructions to git clone the master Galaxy (Feb., 2016) and configured it for local production use with PostgreSQL and proftp. First tried ansible to install the tools, but did not succeed. Then tried the online admin installation of tools one-by-one. That worked, and I installed at least one tool for each section this way. With more help from you and others later, I got ansible-playbook to run to install the tools. That ran OK, but did not see the tools installed show up on the web frontend.

Beginning of the tool_list.yml is the same as the one included in the playbook/roles, except for the api_key and galaxy_instance:

api_key: ‘d22b682…’ galaxy_instance: 127.0.0.1:8080http://127.0.0.1:8080 tools:

- name: ‘column_maker’

owner: …

The command I used is: ansible-playbook tools.yaml The playbook was downloaded end of March, following the link given on the Galaxy tool installation guide. Manual installation of the tools one-by-one from the Admin web page works. The tools installed show up on the web page.

Thanks, Bill From: Marius van den Beek [mailto:m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com] Sent: Thursday, April 21, 2016 9:45 AM To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Enis Afgan <enis.afgan@irb.hrmailto:enis.afgan@irb.hr>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org

Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill, can you describe what exactly you have done? What would be good is if you could post the beginning of your tool_list.yml file, the command that you used to run the playbook, the version of galaxy and the last commit of the playbook you are using (the last entry of `git log`). For any of this to work you should also be able manually install tools from the toolshed. Does this work for you?

On 21 April 2016 at 18:14, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: Does anyone know why Ansible installation of the tools did not update the shed_tools_conf.xml file to reflect the installed tools? How can I make the tools installed with the Ansible playbook visible on the web front end? Thanks, Bill

From: Enis Afgan [mailto:enis.afgan@irb.hrmailto:enis.afgan@irb.hr] Sent: Friday, April 8, 2016 9:19 AM

To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

The location of that dir is defined in shed_tool_conf.xml[.sample] and defaults to ../shed_tools. The reasoning is described here, under item #2: https://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Tool_Shed

On Thu, Apr 7, 2016 at 11:09 AM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote: Thanks, Enis! Yes, that line was uncommented with the option pointing to “tool_conf.xml,shed_tool_conf.xml”. However, I noticed that the “shed_tool_conf.xml” has not been changed after running the ansible-playbook to install tools. One other thing: the shed_tools directory was one level above the Galaxy subdirectories: i.e., all subdirectories (config, database, tool-data, tools, static, etc) are in /home/galaxy/galaxy, while “shed_tools” is in /home/galaxy. Do not know why.

Thanks, Bill

From: Enis Afgan [mailto:enis.afgan@irb.hrmailto:enis.afgan@irb.hr] Sent: Thursday, April 7, 2016 7:06 AM To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Marius van den Beek <m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org

Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill, Do you have the value set in Galaxy's $GALAXY_ROOT/config/galaxy.ini file for setting tool_config_file option? I believe this variable should be set to a file other than the default *.sample.

On Wed, Apr 6, 2016 at 9:21 PM, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> wrote:

Hi, Marius,

I got ansible running and installed the tools on my local instance of Galaxy. However, the tools are not shown on the tool panel on the web page. Wonder if the tools has been installed in the wrong place, or something else is wrong. Have been searching the Wiki and list without any resulst. Please point me to the right directions.

Thanks,

Bill

From: Marius van den Beek [mailto:m.vandenbeek@gmail.commailto:m.vandenbeek@gmail.com] Sent: Friday, March 4, 2016 12:27 PM To: William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> Cc: Dannon Baker <dannon.baker@gmail.commailto:dannon.baker@gmail.com>; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

On 4 March 2016 at 20:47, William Ge <wge@centrilliontech.commailto:wge@centrilliontech.com> 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 dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going.

If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki).

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h Traceback (most recent call last): File "files/install_tool_shed_tools.py", line 49, in <module> logging.captureWarnings(True) # Capture HTTPS warngings from urllib3 AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/