tool_dependency_dir (Installed, missing tool dependencies)

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tool_dependency_dir (Installed, missing tool dependencies)

Wang, Xiaofei
Dear there,

I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing".

Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this:

#Path to the directory in which managed tool dependencies are placed.  To use
# the dependency system, see the documentation at:
# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
#tool_dependency_dir = None 
tool_dependency_dir = ../tool_dependencies  

Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin "manage installed tool shed repositories", the installation status is "Installed, missing tool dependencies" for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread "The migrated BWA installed but missing dependencies". But, I did not get the idea. 

Could you tell me why this happen and how to fix it up?

Thank you so much!

------------------------------------------------------------------------------------------
Your setting for tool_dependency_dir should not be as you've stated:

tool_dependency_dir = tool_dependencies

It should be an actual path on your local file system, something like:

tool_dependency_dir = ../tool_dependencies

If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory.

I cannot guarantee that this change will solve your problem, but it will be a step in the right direction.  After making this change, let us know if you still see problems.

Greg Von Kuster


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Re: tool_dependency_dir (Installed, missing tool dependencies)

Wang, Xiaofei
Hi folks,

Could anybody answer my question and help me figure it out?

Thank you so much!

Best,

Xiaofei

From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, March 06, 2014 4:41 PM
To: [hidden email]
Subject: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies)

Dear there,

I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing".

Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this:

#Path to the directory in which managed tool dependencies are placed.  To use
# the dependency system, see the documentation at:
# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
#tool_dependency_dir = None 
tool_dependency_dir = ../tool_dependencies  

Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin "manage installed tool shed repositories", the installation status is "Installed, missing tool dependencies" for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread "The migrated BWA installed but missing dependencies". But, I did not get the idea. 

Could you tell me why this happen and how to fix it up?

Thank you so much!

------------------------------------------------------------------------------------------
Your setting for tool_dependency_dir should not be as you've stated:

tool_dependency_dir = tool_dependencies

It should be an actual path on your local file system, something like:

tool_dependency_dir = ../tool_dependencies

If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory.

I cannot guarantee that this change will solve your problem, but it will be a step in the right direction.  After making this change, let us know if you still see problems.

Greg Von Kuster


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tool_dependency_dir (Installed, missing tool dependencies)

Greg Von Kuster
In reply to this post by Wang, Xiaofei
<base href="x-msg://232/">Hello,

It's difficult to determine the cause of the problem in your environment based on the details you've provided.  If you have defined your tool_dependeny_dir configuration setting in your universe_wsgi.ini to be ../tool_dependencies, then the tool shed installation process will install tool dependencies there.  If you see them installed elsewhere, then that setting must have been set differently at the time they were installed.  You can try setting it to the location where your tool dependencies have been installed (i.e., the Galaxy installation directory), restat your server and uninstall them.  Then you can reset it to the more appropriate location (e.g., ../tool_dependencies), restart yiour server and reinstall them.  If you have tool dependencies installed in multiple locations, you'll have to be careful to use a process that will eventually result in all tool dependencies installed into a single location.

Greg Von Kuster


On Mar 6, 2014, at 5:41 PM, "Wang, Xiaofei" <[hidden email]> wrote:

Dear there,

I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing".

Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this:

#Path to the directory in which managed tool dependencies are placed.  To use
# the dependency system, see the documentation at:
#tool_dependency_dir = None 
tool_dependency_dir = ../tool_dependencies  

Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin "manage installed tool shed repositories", the installation status is "Installed, missing tool dependencies" for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread "The migrated BWA installed but missing dependencies". But, I did not get the idea. 

Could you tell me why this happen and how to fix it up?

Thank you so much!

------------------------------------------------------------------------------------------
Your setting for tool_dependency_dir should not be as you've stated:

tool_dependency_dir = tool_dependencies

It should be an actual path on your local file system, something like:

tool_dependency_dir = ../tool_dependencies

If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory.

I cannot guarantee that this change will solve your problem, but it will be a step in the right direction.  After making this change, let us know if you still see problems.

Greg Von Kuster

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tool_dependency_dir (Installed, missing tool dependencies)

Wang, Xiaofei
Hi Greg,

I figured it out. I forgot to check the box "Check to uninstall or leave blank to deactivate ". 

I need to uninstall the tool shed but I leave the box blank firstly. So, it is not uninstalled but just deactivated.

Thank you so much!

From: Greg Von Kuster [[hidden email]]
Sent: Tuesday, March 11, 2014 8:47 AM
To: Wang, Xiaofei
Cc: [hidden email]
Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies)

Hello,

It's difficult to determine the cause of the problem in your environment based on the details you've provided.  If you have defined your tool_dependeny_dir configuration setting in your universe_wsgi.ini to be ../tool_dependencies, then the tool shed installation process will install tool dependencies there.  If you see them installed elsewhere, then that setting must have been set differently at the time they were installed.  You can try setting it to the location where your tool dependencies have been installed (i.e., the Galaxy installation directory), restat your server and uninstall them.  Then you can reset it to the more appropriate location (e.g., ../tool_dependencies), restart yiour server and reinstall them.  If you have tool dependencies installed in multiple locations, you'll have to be careful to use a process that will eventually result in all tool dependencies installed into a single location.

Greg Von Kuster


On Mar 6, 2014, at 5:41 PM, "Wang, Xiaofei" <[hidden email]> wrote:

Dear there,

I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing".

Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this:

#Path to the directory in which managed tool dependencies are placed.  To use
# the dependency system, see the documentation at:
#tool_dependency_dir = None 
tool_dependency_dir = ../tool_dependencies  

Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin "manage installed tool shed repositories", the installation status is "Installed, missing tool dependencies" for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread "The migrated BWA installed but missing dependencies". But, I did not get the idea. 

Could you tell me why this happen and how to fix it up?

Thank you so much!

------------------------------------------------------------------------------------------
Your setting for tool_dependency_dir should not be as you've stated:

tool_dependency_dir = tool_dependencies

It should be an actual path on your local file system, something like:

tool_dependency_dir = ../tool_dependencies

If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory.

I cannot guarantee that this change will solve your problem, but it will be a step in the right direction.  After making this change, let us know if you still see problems.

Greg Von Kuster

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

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