[galaxy-dev] PSU Meet and Greet this Saturday

[Suderman Keith]

Sorry for spamming the list, but I thought this would be the easiest/quickest 
way to reach out to any interested people in State College.

I had to make a short-notice trip to meet with colleagues in Pittsburgh and I 
will be driving home to NY Saturday.  Since I am driving right by State College 
I thought it would be silly, if not downright rude, if I didn’t at least ask if 
anyone is up for a quick meet and greet somewhere?  I should be passing by 
around 1-2PM.

I would like to put some faces to the names I see on the list and you guys 
might be interested in learning more about what the NLP community is doing with 
Galaxy.

Cheers,
Keith

--
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY



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

[William Ge]

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.vandenb...@gmail.com]
Sent: Thursday, April 21, 2016 10:39 AM
To: William Ge 
Cc: Enis Afgan ; 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 
mailto:m.vandenb...@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 - 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 
mailto:w...@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.vandenb...@gmail.com]
Sent: Thursday, April 21, 2016 9:45 AM
To: William Ge mailto:w...@centrilliontech.com>>
Cc: Enis Afgan mailto:enis.af...@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 
mailto:w...@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.af...@irb.hr]
Sent: Friday, April 8, 2016 9:19 AM

To: William Ge mailto:w...@centrilliontech.com>>
Cc: Marius van den Beek 
mailto:m.vandenb...@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 
mailto:w...@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.af...@irb.hr

[galaxy-dev] Main Toolshed Account password reset

[Oksana Korol]

Sorry for the previous email's subject line. Re-sending the questions with
the proper subject.

Hi,

Who is the administrator on Galaxy Main Toolshed (
https://toolshed.g2.bx.psu.edu)? I'm trying to re-set a password for the
work Galaxy toolshed account, but I think that the email is blocked by our
firewall. Who can I contact to resolve this issue?

Thanks!

-- 
::
Oksana Korol
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[Marius van den Beek]

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 
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 - 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  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.vandenb...@gmail.com]
>> *Sent:* Thursday, April 21, 2016 9:45 AM
>> *To:* William Ge 
>> *Cc:* Enis Afgan ; 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  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.af...@irb.hr]
>> *Sent:* Friday, April 8, 2016 9:19 AM
>>
>>
>> *To:* William Ge 
>> *Cc:* Marius van den Beek ;
>> 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 
>> 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.af...@irb.hr]
>> *Sent:* Thursday, April 7, 2016 7:06 AM
>> *To:* William Ge 
>> *Cc:* Marius van den Beek ;
>> 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 
>> 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 v

Re: [galaxy-dev] galaxy-dev Digest, Vol 118, Issue 18

[Oksana Korol]

Hi,

Who is the administrator on Galaxy Main Toolshed (
https://toolshed.g2.bx.psu.edu)? I'm trying to re-set a password for the
work Galaxy toolshed account, but I think that the email is blocked by our
firewall. Who can I contact to resolve this issue?

Thanks!
Oksana Korol
___
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/

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

[Marius van den Beek]

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 - 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  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.vandenb...@gmail.com]
> *Sent:* Thursday, April 21, 2016 9:45 AM
> *To:* William Ge 
> *Cc:* Enis Afgan ; 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  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.af...@irb.hr]
> *Sent:* Friday, April 8, 2016 9:19 AM
>
>
> *To:* William Ge 
> *Cc:* Marius van den Beek ;
> 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 
> 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.af...@irb.hr]
> *Sent:* Thursday, April 7, 2016 7:06 AM
> *To:* William Ge 
> *Cc:* Marius van den Beek ;
> 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 
> 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.vandenb...@gmail.com]
> *Sent:* Friday, March 4, 2016 12:27 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
>
>
>
> On 4 March 2016 at 20:47, William Ge  wrote:
>
> Thanks a lot, Marius!
>
> Sure, you're welcome

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

[William Ge]

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.vandenb...@gmail.com]
Sent: Thursday, April 21, 2016 9:45 AM
To: William Ge 
Cc: Enis Afgan ; 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 
mailto:w...@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.af...@irb.hr]
Sent: Friday, April 8, 2016 9:19 AM

To: William Ge mailto:w...@centrilliontech.com>>
Cc: Marius van den Beek 
mailto:m.vandenb...@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 
mailto:w...@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.af...@irb.hr]
Sent: Thursday, April 7, 2016 7:06 AM
To: William Ge mailto:w...@centrilliontech.com>>
Cc: Marius van den Beek 
mailto:m.vandenb...@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 
mailto:w...@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.vandenb...@gmail.com]
Sent: Friday, March 4, 2016 12:27 PM
To: William Ge mailto:w...@centrilliontech.com>>
Cc: Dannon Baker mailto:dannon.ba...@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 
mailto:w...@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. 

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

[Marius van den Beek]

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  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.af...@irb.hr]
> *Sent:* Friday, April 8, 2016 9:19 AM
>
> *To:* William Ge 
> *Cc:* Marius van den Beek ;
> 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 
> 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.af...@irb.hr]
> *Sent:* Thursday, April 7, 2016 7:06 AM
> *To:* William Ge 
> *Cc:* Marius van den Beek ;
> 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 *$GALAXY_ROOT/config/galaxy.ini*
> file for setting *tool_config_file *option? I believe this variable
> should be set to a file other than the default **.sample*.
>
>
>
> On Wed, Apr 6, 2016 at 9:21 PM, William Ge 
> wrote:
>
> Hi, Marius,
>
>
>
> I got ansible running and installed the tools on my local instance of
> Galaxy. However, the tools are not shown on the tool panel on the web page.
> Wonder if the tools has been installed in the wrong place, or something
> else is wrong. Have been searching the Wiki and list without any resulst.
> Please point me to the right directions.
>
>
>
> Thanks,
>
> Bill
>
>
>
> *From:* Marius van den Beek [mailto:m.vandenb...@gmail.com]
> *Sent:* Friday, March 4, 2016 12:27 PM
> *To:* William Ge 
> *Cc:* Dannon Baker ;
> galaxy-dev@lists.galaxyproject.org
> *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
> Ansible Play
>
>
>
> On 4 March 2016 at 20:47, William Ge  wrote:
>
> Thanks a lot, Marius!
>
> Sure, you're welcome!
>
>
>
> I am a newbie to this complex system and want a quick clone/install
> locally. I have spent over two weeks on the process. There are many
> configuration files and environment variables or dependencies to sort out.
> I wish the sample configuration files would include most of the options so
> that new installation just needs to comment out or delete unwanted ones.
>
>
>
> The galaxy team definitely aims for this, and usually you should (tm) be
> able to clone galaxy and use run.sh to get going.
>
> If you can tell us the steps where you were struggling we can try to
> update or clarify the documentation (A lot of it is on the wiki).
>
> Anyway, here is the error I got:
>
> [galaxy@Pegasus ansible-galaxy-tools]$ python
> files/install_tool_shed_tools.py -h
> Traceback (most recent call last):
>   File "files/install_tool_shed_tools.py", line 49, in 
> 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/
>
>
>
>
>
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To search Galaxy mailing li

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

[William Ge]

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.af...@irb.hr]
Sent: Friday, April 8, 2016 9:19 AM
To: William Ge 
Cc: Marius van den Beek ; 
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 
mailto:w...@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.af...@irb.hr]
Sent: Thursday, April 7, 2016 7:06 AM
To: William Ge mailto:w...@centrilliontech.com>>
Cc: Marius van den Beek 
mailto:m.vandenb...@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 
mailto:w...@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.vandenb...@gmail.com]
Sent: Friday, March 4, 2016 12:27 PM
To: William Ge mailto:w...@centrilliontech.com>>
Cc: Dannon Baker mailto:dannon.ba...@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 
mailto:w...@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 
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?

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Re: [galaxy-dev] [SPAM] RE: GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile Devices; and Tools, Tools, Tools!

[Hans-Rudolf Hotz]

https://connect.johnshopkins.edu/gxyadmins201604/

it is also on the wiki



On 04/21/2016 04:47 PM, Christian Brenninkmeijer wrote:

Can someone please post the joining URL.
Thanks
Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Hotz, Hans-Rudolf [hansrudolf.h...@fmi.ch]
Sent: Monday, April 18, 2016 10:06 AM
To: galaxy-dev@lists.galaxyproject.org
Cc: Hans-Rudolf Hotz
Subject: [galaxy-dev] GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile 
Devices; and Tools, Tools, Tools!

Hello all,

The next  
GalaxyAdmins online 
meetup is this 
Thursday, April 21 at 5PM CET (see your local time to know when to 
connect):

The featured topics are:


The Galaxy Portal: Accessing Galaxy from Mobile 
Devices

Ivar Grytten and Geir Kjetil 
Sandve, University of 
Oslo

Tool Development Developments
John Chilton, Penn State 
University

The meetup will use the same Adobe Connect technology used on previous calls. 
The 'Meeting Room Link' will be provided on the wiki page in time. It takes a 
couple of minutes to connect, so you are encouraged to start connecting a few 
minutes early.

See http://bit.ly/gxyadm201604 for full details.

Thanks,

Dave C and Hans-Rudolf

GalaxyAdmins is a 
discussion group for Galaxy community members who are responsible for Galaxy 
installations.
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Re: [galaxy-dev] GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile Devices; and Tools, Tools, Tools!

[Christian Brenninkmeijer]

Can someone please post the joining URL.
Thanks
Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Hotz, Hans-Rudolf [hansrudolf.h...@fmi.ch]
Sent: Monday, April 18, 2016 10:06 AM
To: galaxy-dev@lists.galaxyproject.org
Cc: Hans-Rudolf Hotz
Subject: [galaxy-dev] GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile 
Devices; and Tools, Tools, Tools!

Hello all,

The next 
 
GalaxyAdmins
 online 
meetup
 is this Thursday, April 21 at 5PM CET (see your local 
time to know when to connect):

The featured topics are:


The Galaxy Portal: Accessing Galaxy from Mobile 
Devices

Ivar Grytten and Geir 
Kjetil Sandve, University 
of Oslo

Tool Development Developments
John Chilton, Penn State 
University

The meetup will use the same Adobe Connect technology used on previous calls. 
The 'Meeting Room Link' will be provided on the wiki page in time. It takes a 
couple of minutes to connect, so you are encouraged to start connecting a few 
minutes early.

See http://bit.ly/gxyadm201604 for full details.

Thanks,

Dave C and Hans-Rudolf

GalaxyAdmins is a 
discussion group for Galaxy community members who are responsible for Galaxy 
installations.
___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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