Hi Jim,

thanks very much for catching this and providing the fix (I've been away from 
email for a few days, so am just getting caught up).  I've committed this in 
change set 7705:ba64c2178fbe.

Greg Von Kuster


On Sep 17, 2012, at 5:13 PM, Jim Johnson wrote:

> Greg,
> 
> I think  templates/admin/tool_shed_repository/common.mako  
> needs to bypass the 'set_environment' requirement in the following block.
> 
> Thanks,
> 
> JJ
> 
> 
> 
> $ hg diff templates/admin/tool_shed_repository/common.mako
> diff -r 65ecf4e0ed28 templates/admin/tool_shed_repository/common.mako
> --- a/templates/admin/tool_shed_repository/common.mako  Mon Sep 17 16:24:27 
> 2012 -0400
> +++ b/templates/admin/tool_shed_repository/common.mako  Mon Sep 17 16:06:52 
> 2012 -0500
> @@ -129,28 +129,30 @@
>                                  <% package_header_row_displayed = True %>
>                              %endif
>                              %for dependency_key, requirements_dict in 
> tool_dependencies.items():
> -                                <%
> -                                    name = requirements_dict[ 'name' ]
> -                                    version = requirements_dict[ 'version' ]
> -                                    type = requirements_dict[ 'type' ]
> -                                    install_dir = os.path.join( 
> trans.app.config.tool_dependency_dir,
> -                                                                name,
> -                                                                version,
> -                                                                
> repository_owner,
> -                                                                
> repository_name,
> -                                                                
> changeset_revision )
> -                                    tool_dependency_readme_text = 
> requirements_dict.get( 'readme', None )
> -                                %>
> -                                %if not os.path.exists( install_dir ):
> -                                    <tr>
> -                                        <td>${name}</td>
> -                                        <td>${version}</td>
> -                                        <td>${type}</td>
> -                                        <td>${install_dir}</td>
> -                                    </tr>
> -                                    %if tool_dependency_readme_text:
> -                                        <tr><td colspan="4" 
> bgcolor="#FFFFCC">${name} ${version} requirements and installation 
> information</td></tr>
> -                                        <tr><td 
> colspan="4"><pre>${tool_dependency_readme_text}</pre></td></tr>
> +                                %if not dependency_key == 'set_environment':
> +                                    <%
> +                                        name = requirements_dict[ 'name' ]
> +                                        version = requirements_dict[ 
> 'version' ]
> +                                        type = requirements_dict[ 'type' ]
> +                                        install_dir = os.path.join( 
> trans.app.config.tool_dependency_dir,
> +                                                                    name,
> +                                                                    version,
> +                                                                    
> repository_owner,
> +                                                                    
> repository_name,
> +                                                                    
> changeset_revision )
> +                                        tool_dependency_readme_text = 
> requirements_dict.get( 'readme', None )
> +                                    %>
> +                                    %if not os.path.exists( install_dir ):
> +                                        <tr>
> +                                            <td>${name}</td>
> +                                            <td>${version}</td>
> +                                            <td>${type}</td>
> +                                            <td>${install_dir}</td>
> +                                        </tr>
> +                                        %if tool_dependency_readme_text:
> +                                            <tr><td colspan="4" 
> bgcolor="#FFFFCC">${name} ${version} requirements and installation 
> information</td></tr>
> +                                            <tr><td 
> colspan="4"><pre>${tool_dependency_readme_text}</pre></td></tr>
> +                                        %endif
>                                      %endif
>                                  %endif
>                              %endfor
> 
> 
> 
> 
> On 9/16/12 8:48 AM, Jim Johnson wrote:
>> Greg, Pablo,
>> 
>> I'm using a SnpEffect repository 'snpeff_with_dep'  in 
>> http://testtoolshed.g2.bx.psu.edu/  
>> to test using tool_dependencies.xml with the <set_environment> tag.
>> ( You both write access, if you want to use this for correcting my errors or 
>> debugging. )
>> 
>> I'm getting an error in prepare_for_install:
>> 
>> Module galaxy.web.controllers.admin_toolshed:1174 in prepare_for_install
>> >>> tool_dependencies
>> {'set_environment': [{'type': 'environment variable', 'name': 
>> 'JAVA_JAR_PATH'}], 'snpEff/3.0f': {'readme': '\n        ', 'version': 
>> '3.0f', 'type': 'package', 'name': 'snpEff'}}
>> ...
>> Module _admin_tool_shed_repository_common_mako:242 in 
>> render_render_tool_dependency_section
>> >>  name = requirements_dict[ 'name' ]
>> TypeError: list indices must be integers, not str 
>> 
>> It appears that the requirements_dict for the set_environment tag is 
>> enclosed in an array.   
>> I haven't yet looked at the repository code to see how that might happen.
>> 
>> 
>> Pablo,
>> 
>> The http://sourceforge.net/projects/snpeff/files/  repository should 
>> probably have versions packaged for download named like:
>> 
>>   http://sourceforge.net/projects/snpeff/files/snpEff_3_0.tgz
>> 
>>   $ tar ztvf snpEff_3_0.tgz
>>   drwxrwxrwx  0 0      0           0 Aug 23 12:17 snpEff_3_0/
>>   -rwxrwxrwx  0 0      0    14298767 Aug 23 12:17 snpEff_3_0/SnpSift.jar
>>   ...
>> 
>> That will allow versioning within galaxy, and successive versions of 
>> tool_dependencies.xml with only need a change to the action tag:   
>> download_by_url
>>   
>> Thanks,
>> 
>> JJ
>> 
>> 
>> 
>> I'm trying to test a repository that use  in tool_depen
>>> 
>>> Message: 18
>>> Date: Thu, 13 Sep 2012 11:46:32 -0400
>>> From: Greg Von Kuster <g...@bx.psu.edu>
>>> To: David Hoover <hoove...@helix.nih.gov>
>>> Cc: galaxy-dev@lists.bx.psu.edu
>>> Subject: Re: [galaxy-dev] environment variables and paths for toolshed
>>>     tools
>>> Message-ID: <f75d6320-3af8-4bb0-8f31-b0f44aa13...@bx.psu.edu>
>>> Content-Type: text/plain; charset="us-ascii"
>>> 
>>> Hello David,
>>> 
>>> I've just committed change set 7656:6aadac8026cb to the Galaxy central 
>>> repository that provides the ability to do what you need here.  It would be 
>>> great if you could try things out and let me know if you run into any 
>>> problems.  
>>> 
>>> I've been working with nikhil-joshi's deseq_and_sam2counts repository in 
>>> the main Galaxy tool shed because his tools require this new feature as 
>>> well.  This example should provide you with the information you'll need to 
>>> tweak your tool shed repository so that your tool dependencies are located 
>>> where they get installed rather than attempting to move them to 
>>> ${GALAXY_DATA_INDEX_DIR} or some other location.
>>> 
>>> Here is the tool_dependency.xml file entry for locating a directory 
>>> referred to by an environment variable name R_SCRIPT_PATH.
>>> 
>>> 
>>> <?xml version="1.0"?>
>>> <tool_dependency>
>>>     <set_environment version="1.0">
>>>         <environment_variable name="R_SCRIPT_PATH" 
>>> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
>>>     </set_environment>
>>> </tool_dependency>
>>> 
>>> 
>>> The <set_enviroment> tag, is still supported inside <package> tag sets, but 
>>> when defined at the xml root level, it will locate dependencies included in 
>>> the installed tool shed repository.  Of course, the above 
>>> tool_dependencies.xml file could of course also include entries for tool 
>>> dependencies that are packages, For example:
>>> 
>>> 
>>> <?xml version="1.0"?>
>>> <tool_dependency>
>>>     <set_environment version="1.0">
>>>         <environment_variable name="R_SCRIPT_PATH" 
>>> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
>>>     </set_environment>
>>>     <package name="R" version="2.15.1">
>>>         <install version="1.0">
>>>             <actions>
>>>                 <action 
>>> type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
>>>                 <action type="shell_command">./configure 
>>> --prefix=$INSTALL_DIR</action>
>>>                 <action type="shell_command">make</action>
>>>                 <action type="set_environment">
>>>                     <environment_variable name="PATH" 
>>> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>>>                 </action>
>>>             </actions>
>>>         </install>
>>>         <readme>
>>> You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to 
>>> build R.
>>>         </readme>
>>>     </package>
>>> </tool_dependency>
>>> 
>>> These tool dependency definitions are handled as described in the following 
>>> section of the tool shed wiki:
>>> 
>>> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
>>> 
>>> So in order for the dependencies to be handled when the repository is 
>>> installed, they must be defined in at least one of the <requirement> tag 
>>> sets in at least 1 tool config in the repository.  So, the <requirements> 
>>> tag set in the deseq.xml tool config file will look something like this 
>>> (there are more requirement tags defined here than in the 
>>> tool_dependencies.xml fiel above, but you should get the idea).
>>> 
>>> 
>>>     <requirements>
>>>         <requirement type="set_environment">R_SCRIPT_PATH</requirement>
>>>         <requirement type="package" version="2.15.1">R</requirement>
>>>         <requirement type="package" 
>>> version="2.10">Bioconductor</requirement>
>>>         <requirement type="package" version="1.8.3">DESeq</requirement>
>>>         <requirement type="package" 
>>> version="1.24.0">aroma.light</requirement>
>>>         <requirement type="package" version="0.20-6">lattice</requirement>
>>>     </requirements>
>>> 
>>> 
>>> The <command> tag set in the deseq.xml tool config is also slightly 
>>> altered.  Here is the way it looks before using this new approach:
>>> 
>>> <command interpreter="python">
>>>          stderr_wrapper.py Rscript ${GALAXY_DATA_INDEX_DIR}/deseq.R $counts 
>>> $column_types $comparison $top_table $diagnostic_html 
>>> "$diagnostic_html.files_path" "$counts.name"
>>> </command>
>>> 
>>> To use this new feature, the command string now uses the R_SCRIPT_PATH 
>>> environment variable ( notice the required backslash to escape the $ )
>>> 
>>> 
>>> <command interpreter="python">
>>>     stderr_wrapper.py Rscript \$R_SCRIPT_PATH/deseq.R $counts $column_types 
>>> $comparison $top_table $diagnostic_html "$diagnostic_html.files_path" 
>>> "$counts.name"
>>> </command>
>>> 
>>> When installed from the tool shed, a tool dependency object named 
>>> R_SCRIPT_PATH will be created and associated with the installed repository. 
>>>  The dependency will have a pointer to the env.sh file that is created to 
>>> set the value of the R_SCRIPT_PATH environment variable.
>>> 
>>> Let me know if you bump into any issues in getting this working for your 
>>> tools.
>>> 
>>> Thanks!
>>> 
>>> Greg Von Kuster
>>> 
>>> 
>>> On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
>>> 
>>>> Are there any environment variables that are honored by toolshed installed 
>>>> tools?  I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or 
>>>> $GALAXY_HOME, then uploaded it the test toolshed, then installed it 
>>>> automatically.  Neither of these resolved to what I expected.  I don't 
>>>> want to hard-code the path in the xml tool file, but rather have a default 
>>>> location for other executables and jar files.  How should this best be 
>>>> done?
>>>> 
>>>> David Hoover
>>>> Helix Systems Staff
>>>> ___________________________________________________________
>>>> 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/
>> 
> 
> <common.mako.diff>___________________________________________________________
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> 
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