subject:"\[galaxy\-dev\] Error installing tools from toolshed"

Re: [galaxy-dev] Error installing tools from toolshed

2015-11-30 Thread Scott Szakonyi

Nicola,

Sorry for the delay... holidays here in the US. That worked perfectly...
thank you very much!

Best,

Scott

On Fri, Nov 20, 2015 at 1:59 PM, Nicola Soranzo  wrote:

> Hi Scott,
> you can try to reinstall it with: "Admin" -> "Manage installed tools",
> then click on "Advanced Search" on top, then click on "Deactivated or
> uninstalled" and click on "Activate or reinstall" on Trimmomatic menu.
>
> Cheers,
> Nicola
>
>
> On 20/11/15 18:07, Scott Szakonyi wrote:
>
> Hi Nicola,
>
> Certainly. On screen, I get a message that says "Revision *f8a9a5eaca8a* of
> repository *trimmomatic* owned by *pjbriggs* has already been installed."
>
> In the logs:
>
> 129.74.33.163 - - [20/Nov/2015:12:51:44 -0400] "GET
> /admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.
> HTTP/1.1" 200 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/install_latest_repository_revision?id=d071e794759ab192
> HTTP/1.1" 302 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.
> HTTP/1.1" 200 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/browse_repositories?operation=install+latest+revision=d071e794759ab192
> HTTP/1.1" 302 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
>
> I'm not 100% sure these are in order... I have multiple web handlers
> running and the requests get spread out between them. I've tried to order
> them as best I can.
>
> Thanks!
>
> Scott
>
> On Fri, Nov 20, 2015 at 12:31 PM, Nicola Soranzo 
> wrote:
>
>> Hi Scott,
>> can you try to update Trimmomatic (i.e. go to "Admin" -> "Manage
>> installed tools" and click on "Install latest revision" on Trimmomatic
>> menu) ?
>> If this does not work, copy the relevant log from the Galaxy server and
>> post it on the mailing list.
>>
>> Cheers,
>> Nicola
>>
>>
>> On 20/11/15 17:23, Scott Szakonyi wrote:
>>
>> I was able to switch over to GitHub without issue. Thanks for pointing me
>> in the right direction.
>>
>> I have installed Trimmomatic successfully, although I wasn't able to
>> install the latest version. If I try to install the "2015-09-23" revision,
>> I get "Internal Server Error Galaxy was unable to successfully complete
>> your request". The "2015-04-22" revision installs without issue.
>>
>> I'm still having troubles with Picard as well, but one thing at a time!
>> What information can I provide that might help with getting the latest
>> issue of Trimmomatic?
>>
>> Thanks!
>>
>> On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo < 
>> nsora...@tiscali.it> wrote:
>>
>>> Hi Scott,
>>> the mercurial mirror is not up to date unfortunately, see this previous
>>> discussion:
>>>
>>>
>>> http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html
>>>
>>> Cheers,
>>> Nicola
>>>
>>>
>>> On 20/11/15 13:13, Scott Szakonyi wrote:
>>>
>>> Hi Nicola,
>>>
>>> I'm not entirely sure which version... but I am still using the
>>> mercurial mirror, which says I'm up to date. Would this be a wise time,
>>> then, to change over to the Git repository directly?
>>>
>>> Thanks!
>>>
>>> Scott
>>>
>>> On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo < 
>>> nsora...@tiscali.it> wrote:
>>>
 Hi Scott,
 which Galaxy release are you using?
 This is a bug which should be fixed in an updated release_15.07 git
 branch.

 Cheers,
 Nicola

  Scott Szakonyi

Re: [galaxy-dev] Error installing tools from toolshed

2015-11-20 Thread Nicola Soranzo


Hi Scott,
the mercurial mirror is not up to date unfortunately, see this previous 
discussion:


http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html

Cheers,
Nicola

On 20/11/15 13:13, Scott Szakonyi wrote:

Hi Nicola,

I'm not entirely sure which version... but I am still using the 
mercurial mirror, which says I'm up to date. Would this be a wise 
time, then, to change over to the Git repository directly?


Thanks!

Scott

On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo > wrote:


Hi Scott,
which Galaxy release are you using?
This is a bug which should be fixed in an updated release_15.07
git branch.

Cheers,
Nicola

 Scott Szakonyi ha scritto 


Hello all,

I'm having issues installing Trimmomatic and Picard tools from the
toolshed. The errors are of the following form (Trimmomatic used
for the example).

Trimmomatic 0.32 package shows an installation error.

Error details:
File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 142, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package( tool_shed_repository, 
tool_dependency, actions_dict )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 136, in install_and_build_package
dir = tmp_dir
  File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
self.gen.throw(type, value, traceback)
  File 
"/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py",
 line 142, in _setenv
yield
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 100, in install_and_build_package
initial_download=True )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
 line 32, in execute_step
initial_download=initial_download )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 685, in execute_step
dir = self.url_download( work_dir, downloaded_filename, url, 
extract=True, checksums=checksums )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 223, in url_download
extraction_path = archive.extract( install_dir )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 89, in extract
os.chmod( absolute_filepath, unix_permissions )

[Errno 2] No such file or directory: 
'/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/'

I've tried several version of the tool with no success. Any
thoughts? I've searched project website but haven't come up with
anything definitive.

Thanks for any help you can offer,

-- 
Scott B. Szakonyi

Research Programmer
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu 




--
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu 


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Re: [galaxy-dev] Error installing tools from toolshed

2015-11-20 Thread Nicola Soranzo

Hi Scott,
please always reply to the mailing list, because I may not be able to 
solve your issues.

I was able to install the latest revision of Trimmomatic without issues, 
so we may need some more information from the Galaxy logs to understand 
what is your issue.

Same for the other repositories.

Cheers,
Nicola

On 20/11/15 16:09, Scott Szakonyi wrote:

Hi Nicola,

I was able to switch over to GitHub without issue. Thanks for pointing 
me in the right direction.

I have installed Trimmomatic successfully, although I wasn't able to 
install the latest version. If I try to install the "2015-09-23" 
revision, I get "Internal Server Error Galaxy was unable to 
successfully complete your request". The "2015-04-22" revision 
installs without issue.

However, I'm still having problems with the Picard tool. I've tried 
sever of the revisions, and have similar issues with all. Dependencies 
are not installing correctly, and I'm unable to repair them or 
otherwise resolve the problem. Three of the tools that install with 
Picard end up missing dependencies: package_cairo_1_12_14, 
package_pixman_0_32_4, and package_readline_6_2. The underlying errors 
do not seem to have a definite pattern, as was the case when I was 
having problems before the GitHub switch. Is this something that I 
should take up with whoever provides the Picard tool?

Thanks!

Scott

On Fri, Nov 20, 2015 at 9:39 AM, Scott Szakonyi 
> wrote:

Hi Nicola,

Thank you, that's very helpful. I'll switch over to the GitHub
repository and get the latest revision, then we'll see if that
doesn't solve the problem.

Best,

Scott

On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo
> wrote:

Hi Scott,
the mercurial mirror is not up to date unfortunately, see this
previous discussion:

http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html

Cheers,
Nicola

On 20/11/15 13:13, Scott Szakonyi wrote:

Hi Nicola,

I'm not entirely sure which version... but I am still using
the mercurial mirror, which says I'm up to date. Would this
be a wise time, then, to change over to the Git repository
directly?

Thanks!

Scott

On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo
> wrote:

Hi Scott,
which Galaxy release are you using?
This is a bug which should be fixed in an updated
release_15.07 git branch.

Cheers,
Nicola

 Scott Szakonyi ha scritto 

Hello all,

I'm having issues installing Trimmomatic and Picard tools
from the toolshed. The errors are of the following form
(Trimmomatic used for the example).

Trimmomatic 0.32 package shows an installation error.

Error details:
File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 142, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package( 
tool_shed_repository, tool_dependency, actions_dict )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 136, in install_and_build_package
dir = tmp_dir
  File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
self.gen.throw(type, value, traceback)
  File 
"/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py",
 line 142, in _setenv
yield
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 100, in install_and_build_package
initial_download=True )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
 line 32, in execute_step
initial_download=initial_download )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 685, in execute_step
dir = self.url_download( work_dir, downloaded_filename, url, 
extract=True, checksums=checksums )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 223, in url_download
extraction_path = archive.extract( install_dir )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 89, in extract
os.chmod( absolute_filepath, unix_permissions )

[Errno 2] No such file or directory:

Re: [galaxy-dev] Error installing tools from toolshed

2015-11-20 Thread Scott Szakonyi

I was able to switch over to GitHub without issue. Thanks for pointing me
in the right direction.

I have installed Trimmomatic successfully, although I wasn't able to
install the latest version. If I try to install the "2015-09-23" revision,
I get "Internal Server Error Galaxy was unable to successfully complete
your request". The "2015-04-22" revision installs without issue.

I'm still having troubles with Picard as well, but one thing at a time!
What information can I provide that might help with getting the latest
issue of Trimmomatic?

Thanks!

On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo  wrote:

> Hi Scott,
> the mercurial mirror is not up to date unfortunately, see this previous
> discussion:
>
>
> http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html
>
> Cheers,
> Nicola
>
>
> On 20/11/15 13:13, Scott Szakonyi wrote:
>
> Hi Nicola,
>
> I'm not entirely sure which version... but I am still using the mercurial
> mirror, which says I'm up to date. Would this be a wise time, then, to
> change over to the Git repository directly?
>
> Thanks!
>
> Scott
>
> On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo 
> wrote:
>
>> Hi Scott,
>> which Galaxy release are you using?
>> This is a bug which should be fixed in an updated release_15.07 git
>> branch.
>>
>> Cheers,
>> Nicola
>>
>>  Scott Szakonyi ha scritto 
>>
>>
>> Hello all,
>>
>> I'm having issues installing Trimmomatic and Picard tools from the
>> toolshed. The errors are of the following form (Trimmomatic used for the
>> example).
>>
>> Trimmomatic 0.32 package shows an installation error.
>>
>> Error details:
>>
>> File 
>> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>>  line 142, in install_and_build_package_via_fabric
>>
>> tool_dependency = self.install_and_build_package( tool_shed_repository, 
>> tool_dependency, actions_dict )
>>
>>   File 
>> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>>  line 136, in install_and_build_package
>> dir = tmp_dir
>>   File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
>> self.gen.throw(type, value, traceback)
>>
>>   File 
>> "/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py",
>>  line 142, in _setenv
>> yield
>>
>>   File 
>> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>>  line 100, in install_and_build_package
>> initial_download=True )
>>
>>   File 
>> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
>>  line 32, in execute_step
>> initial_download=initial_download )
>>
>>   File 
>> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
>>  line 685, in execute_step
>>
>> dir = self.url_download( work_dir, downloaded_filename, url, 
>> extract=True, checksums=checksums )
>>
>>   File 
>> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
>>  line 223, in url_download
>> extraction_path = archive.extract( install_dir )
>>
>>   File 
>> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
>>  line 89, in extract
>> os.chmod( absolute_filepath, unix_permissions )
>>
>>
>> [Errno 2] No such file or directory: 
>> '/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/'
>>
>> I've tried several version of the tool with no success. Any thoughts?
>> I've searched project website but haven't come up with anything definitive.
>>
>> Thanks for any help you can offer,
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>>
>>
>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
>
>


-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
___
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:
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Re: [galaxy-dev] Error installing tools from toolshed

2015-11-20 Thread Nicola Soranzo

Hi Scott,
you can try to reinstall it with: "Admin" -> "Manage installed tools", 
then click on "Advanced Search" on top, then click on "Deactivated or 
uninstalled" and click on "Activate or reinstall" on Trimmomatic menu.

Cheers,
Nicola

On 20/11/15 18:07, Scott Szakonyi wrote:

Hi Nicola,

Certainly. On screen, I get a message that says "Revision 
*f8a9a5eaca8a* of repository *trimmomatic* owned by *pjbriggs* has 
already been installed."

In the logs:

129.74.33.163 - - [20/Nov/2015:12:51:44 -0400] "GET 
/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed. 
HTTP/1.1" 200 - 
"https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories; "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML, like 
Gecko) Chrome/46.0.2490.80 Safari/537.36"
129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET 
/admin_toolshed/install_latest_repository_revision?id=d071e794759ab192 
HTTP/1.1" 302 - 
"https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.; 
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 
(KHTML, like Gecko) Chrome/46.0.2490.80 Safari/537.36"
129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET 
/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed. 
HTTP/1.1" 200 - 
"https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.; 
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 
(KHTML, like Gecko) Chrome/46.0.2490.80 Safari/537.36"
129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET 
/admin_toolshed/browse_repositories?operation=install+latest+revision=d071e794759ab192 
HTTP/1.1" 302 - 
"https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.; 
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 
(KHTML, like Gecko) Chrome/46.0.2490.80 Safari/537.36"

I'm not 100% sure these are in order... I have multiple web handlers 
running and the requests get spread out between them. I've tried to 
order them as best I can.

Thanks!

Scott

On Fri, Nov 20, 2015 at 12:31 PM, Nicola Soranzo > wrote:

Hi Scott,
can you try to update Trimmomatic (i.e. go to "Admin" -> "Manage
installed tools" and click on "Install latest revision" on
Trimmomatic menu) ?
If this does not work, copy the relevant log from the Galaxy
server and post it on the mailing list.

Cheers,
Nicola

On 20/11/15 17:23, Scott Szakonyi wrote:

I was able to switch over to GitHub without issue. Thanks for
pointing me in the right direction.

I have installed Trimmomatic successfully, although I wasn't able
to install the latest version. If I try to install the
"2015-09-23" revision, I get "Internal Server Error Galaxy was
unable to successfully complete your request". The "2015-04-22"
revision installs without issue.

I'm still having troubles with Picard as well, but one thing at a
time! What information can I provide that might help with getting
the latest issue of Trimmomatic?

Thanks!

On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo
> wrote:

Hi Scott,
the mercurial mirror is not up to date unfortunately, see
this previous discussion:

http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html

Cheers,
Nicola

On 20/11/15 13:13, Scott Szakonyi wrote:

Hi Nicola,

I'm not entirely sure which version... but I am still using
the mercurial mirror, which says I'm up to date. Would this
be a wise time, then, to change over to the Git repository
directly?

Thanks!

Scott

On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo
> wrote:

Hi Scott,
which Galaxy release are you using?
This is a bug which should be fixed in an updated
release_15.07 git branch.

Cheers,
Nicola

 Scott Szakonyi ha scritto 

Hello all,

I'm having issues installing Trimmomatic and Picard
tools from the

[galaxy-dev] Error installing tools from toolshed

2015-11-19 Thread Scott Szakonyi

Hello all,

I'm having issues installing Trimmomatic and Picard tools from the
toolshed. The errors are of the following form (Trimmomatic used for the
example).

Trimmomatic 0.32 package shows an installation error.

Error details:

File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 142, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package(
tool_shed_repository, tool_dependency, actions_dict )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 136, in install_and_build_package
dir = tmp_dir
  File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
self.gen.throw(type, value, traceback)
  File 
"/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py",
line 142, in _setenv
yield
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 100, in install_and_build_package
initial_download=True )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
line 32, in execute_step
initial_download=initial_download )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 685, in execute_step
dir = self.url_download( work_dir, downloaded_filename, url,
extract=True, checksums=checksums )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 223, in url_download
extraction_path = archive.extract( install_dir )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
line 89, in extract
os.chmod( absolute_filepath, unix_permissions )

[Errno 2] No such file or directory:
'/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/'

I've tried several version of the tool with no success. Any thoughts? I've
searched project website but haven't come up with anything definitive.

Thanks for any help you can offer,

-- 
Scott B. Szakonyi
Research Programmer
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] Error installing tools from toolshed

Re: [galaxy-dev] Error installing tools from toolshed

Re: [galaxy-dev] Error installing tools from toolshed

Re: [galaxy-dev] Error installing tools from toolshed

Re: [galaxy-dev] Error installing tools from toolshed

[galaxy-dev] Error installing tools from toolshed

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