Re: [galaxy-dev] tool_sheds_errors

[Vipin TS]

On Thu, Mar 13, 2014 at 5:32 PM, Wang, Xiaofei  wrote:

>  Hi Folks,
>
>  I figured out the problem of tool dependencies successfully. The
> installation status is installed for all tool sheds. The tools are also
> shown on left tool panel. But, I got problems when I used the tool sheds to
> analyze data.
>
>  For example,
>
>  When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open
> file '~/softwares/shed_tools/
> toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs
> /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory
>
>  When I checked the ~/.../galaxy folder, there are four *.xml files.
> Then, I copied the four files from ~/.../script folder. Now, this tool
> works. But, I don't think this is a right way to figure out this because I
> also got similar problem (I think they are similar) when I used other tool
> sheds as below. So, I am guessing it might be a problem with my configure
> file (universe_wsgi.ini). Could anybody tell me why and how to figure it
> out?
>
>

Hello,
I am responsible for answering the first part of your error message, It is
my mistake that I have to place the right path in the tool configuration
file (xml). This will be fixed soon and update the repository to a new
version.
 regards,
Vipin | Rätsch Lab



>  BWA wrapper error:
> when I used the BWA wrapper for Illunina,
> An error occurred with this dataset:
> Could not determine BWA version
>
> Error indexing reference sequence. /bin/sh: bwa: command not found
>
>  I referred to this link to try to figure out the problem
> http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html.
> But, I think I need more details about the mentioned bwa binaries and path.
>

>  When I used the snpEff, the error is:
>
> Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar
> In fact, the snpEff.jar is located at
>
> ~/softwares/shed_tools/
> toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a
>
>
>  Could you give me some ideas?
>
>
>  Thank you so much!
>
>
>
>
>
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[galaxy-dev] tool_sheds_errors

[Wang, Xiaofei]

Hi Folks,

I figured out the problem of tool dependencies successfully. The installation 
status is installed for all tool sheds. The tools are also shown on left tool 
panel. But, I got problems when I used the tool sheds to analyze data.

For example,

When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open file 
'~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs
/galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory

When I checked the ~/.../galaxy folder, there are four *.xml files. Then, I 
copied the four files from ~/.../script folder. Now, this tool works. But, I 
don't think this is a right way to figure out this because I also got similar 
problem (I think they are similar) when I used other tool sheds as below. So, I 
am guessing it might be a problem with my configure file (universe_wsgi.ini). 
Could anybody tell me why and how to figure it out?

BWA wrapper error:
when I used the BWA wrapper for Illunina,
An error occurred with this dataset:
Could not determine BWA version

Error indexing reference sequence. /bin/sh: bwa: command not found


I referred to this link to try to figure out the problem 
http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html. 
But, I think I need more details about the mentioned bwa binaries and path.


When I used the snpEff, the error is:

Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar

In fact, the snpEff.jar is located at

~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a


Could you give me some ideas?


Thank you so much!






From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, March 11, 2014 8:47 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
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" 
mailto:xfw...@ku.edu>> 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:
# 
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 setti