Hi Greg,

do you mean that patch?

https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc

I can reproduce that error and it is not fixed with latest galaxy-central, or did you only applied it to next-stable?

You can test with my augustus repository if you like. http://toolshed.g2.bx.psu.edu/view/bgruening/augustus

Thanks, Bjoern

Hello Saskia,

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has been committed to the next-stable branch and is currently running on both the test and main Galaxy tool sheds. Thanks for reporting this issue.

Greg Von Kuster

On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann s.hiltemann@erasmusmc.nl wrote:

...

I updated my Galaxies to the latest version today, and when I try to install a toolshed repository which defines an environment variable via the <set_environment> tags in the tool_dependencies.xml file, I get an error (see below).

tool_dependencies.xml:

<?xml version="1.0"?>

<tool_dependency> <set_environment version="1.0"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency>

(before the update these repositories installed without problems)

..doing the same as an action within a package dependency does still work, so for now I have just changed the tools I needed to set the environment this way, e.g.:

<tool_dependency> <package name="condel" version="1"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> Set condel environment variable </readme> </package> </tool_dependency>

Is this the preferred way of doing it, and should I change all my tools this way? or should both ways still be working?

Saskia

Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'env_var_elem' is not defined URL: http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_depende... Module weberror.evalexception.middleware:364 in respond view

...

...

app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__ view

...

...

return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__ view

...

...

return self.application(environ, start_response)

Module galaxy.web.framework.base:132 in __call__ view

...

...

return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:190 in handle_request view

...

...

body = method( trans, **kwargs )

Module galaxy.web.framework:229 in decorator view

...

...

return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in manage_tool_dependencies view

...

...

self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )

Module galaxy.web.framework:229 in decorator view

...

...

return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in initiate_tool_dependency_installation view

...

...

tool_dependencies=tool_dependencies )

Module tool_shed.util.common_install_util:486 in handle_tool_dependencies view

...

...

env_var_name = env_var_elem.get( 'name', None )

NameError: global name 'env_var_elem' is not defined

---

From: S.D. Hiltemann Sent: Friday, August 02, 2013 11:19 AM To: galaxy-dev@lists.bx.psu.edu Subject: Toolshed repository update error

I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing my script to fail of course. How can I prevent this from happening?

Saskia

snippet of the code:

if [[ ! -s $rfile ]] 
then           
    dummycol=${addcols:2}
    outputcol=${dummycol//",B."/"    "}

<<<<<<< local echo -e "${col_chr_name}\t${col_start_name}\t ${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile cat $rfile ======= numcommas=`echo "$addcols" | grep -o "," | wc -l` echo "numcolums: $numcommas"

    awk 'BEGIN{FS="\t";OFS="\t"}{
            if(FNR==1)
                print $0,"'"$outputcol"'"; 
            else{
                printf $0
                for(i=0;i<="'"$numcommas"'"+1;i++)
                    printf "\t"
                printf "\n"
            }
        }END{}' $ofile > tempofile

        mv tempofile $ofile

    return

...

...

...

...

>>> other

fi

---

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---

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Hi Greg,

sorry for the confusion. You answered to Saskia

...

...

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has

If I search for that number I only find your fix for the repository action view. But I'm searching for the fix for ' Installing toolshed repositories with set_environment dependency'. Saskia posted that she gets that error:

NameError: global name 'env_var_elem' is not defined

And I can reproduce it with latest galaxy-central and http://toolshed.g2.bx.psu.edu/view/bgruening/augustus a repository that used to work, so I assume that is a regression.

Sorry for not being clear enough! Cheers, Bjoern

Hello Bjoern,

The changeset to which your link refers is the change that allows anyone that has write permission on a repository to reset all metadata on that repository from the "Repository Actions" pop-up menu on the "View repository" page. Previous to this change, this feature was restricted to the owner of the repository. I committed this changeset to the next-stble branch and merged it into the central branch, so it is available in both.

I have just double-cheked using the central branch on my local development repository, and this feature is working as expected. For example, if I have a repo owned by user test and only test has write permission on that repo, the user test1 cannot reset all metadata on the repo. However, if user test grants write permission on the repo to user test1, then user test1 can immediately reset all metadata on the repo.

Can you let me know what steps you are taking and the behavior you are seeing that differs from this?

Thanks!

Greg Von Kuster

On Oct 29, 2013, at 1:03 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

do you mean that patch?

https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc

I can reproduce that error and it is not fixed with latest galaxy-central, or did you only applied it to next-stable?

You can test with my augustus repository if you like. http://toolshed.g2.bx.psu.edu/view/bgruening/augustus

Thanks, Bjoern

...

Hello Saskia,

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has been committed to the next-stable branch and is currently running on both the test and main Galaxy tool sheds. Thanks for reporting this issue.

Greg Von Kuster

On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann s.hiltemann@erasmusmc.nl wrote:

...

I updated my Galaxies to the latest version today, and when I try to install a toolshed repository which defines an environment variable via the <set_environment> tags in the tool_dependencies.xml file, I get an error (see below).

tool_dependencies.xml:

<?xml version="1.0"?>

<tool_dependency> <set_environment version="1.0"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency>

(before the update these repositories installed without problems)

..doing the same as an action within a package dependency does still work, so for now I have just changed the tools I needed to set the environment this way, e.g.:

<tool_dependency> <package name="condel" version="1"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> Set condel environment variable </readme> </package> </tool_dependency>

Is this the preferred way of doing it, and should I change all my tools this way? or should both ways still be working?

Saskia

Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'env_var_elem' is not defined URL: http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_depende... Module weberror.evalexception.middleware:364 in respond view

...

...

app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__ view

...

...

return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__ view

...

...

return self.application(environ, start_response)

Module galaxy.web.framework.base:132 in __call__ view

...

...

return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:190 in handle_request view

...

...

body = method( trans, **kwargs )

Module galaxy.web.framework:229 in decorator view

...

...

return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in manage_tool_dependencies view

...

...

self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )

Module galaxy.web.framework:229 in decorator view

...

...

return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in initiate_tool_dependency_installation view

...

...

tool_dependencies=tool_dependencies )

Module tool_shed.util.common_install_util:486 in handle_tool_dependencies view

...

...

env_var_name = env_var_elem.get( 'name', None )

NameError: global name 'env_var_elem' is not defined

---

From: S.D. Hiltemann Sent: Friday, August 02, 2013 11:19 AM To: galaxy-dev@lists.bx.psu.edu Subject: Toolshed repository update error

I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing my script to fail of course. How can I prevent this from happening?

Saskia

snippet of the code:

if [[ ! -s $rfile ]] then dummycol=${addcols:2} outputcol=${dummycol//",B."/" "} <<<<<<< local echo -e "${col_chr_name}\t${col_start_name}\t ${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile cat $rfile ======= numcommas=`echo "$addcols" | grep -o "," | wc -l` echo "numcolums: $numcommas"

   awk 'BEGIN{FS="\t";OFS="\t"}{
           if(FNR==1)
               print $0,"'"$outputcol"'"; 
           else{
               printf $0
               for(i=0;i<="'"$numcommas"'"+1;i++)
                   printf "\t"
               printf "\n"
           }
       }END{}' $ofile > tempofile

       mv tempofile $ofile

   return

...

...

>>>>> other

fi

---

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/

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Thanks John,

I just sent my message as yours arrived - this will help me more quickly resolve the issue. I'll have a fix soon.

Greg Von Kuster

On Oct 30, 2013, at 4:09 PM, John Chilton chilton@msi.umn.edu wrote:

I can verify augustus doesn't work correctly any longer, but I do not get the same error. The package installs properly but set_environment doesn't get handled.

As far as I can tell this changeset:

https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8dcfe30fc5b92...

Would break this functionality:

<set_environment version="1.0"> <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment>

(as documented on wiki and as appears in the augustus wrappers).

In particular these three lines:

elif elem.tag == 'set_environment': env_var_name = env_var_elem.get( 'name', None ) if env_var_name:

Which have become:

elif elem.tag == 'set_environment': env_var_name = elem.get( 'name', None ) if env_var_name:

Seem problematic. It looks like the set_environment element doesn't have the name, it is the inner environment_variable elements that do. This should probably be resolved before the next release.

-John

On Wed, Oct 30, 2013 at 10:10 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

sorry for the confusion. You answered to Saskia

...

...

...

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has

If I search for that number I only find your fix for the repository action view. But I'm searching for the fix for ' Installing toolshed repositories with set_environment dependency'. Saskia posted that she gets that error:

NameError: global name 'env_var_elem' is not defined

And I can reproduce it with latest galaxy-central and http://toolshed.g2.bx.psu.edu/view/bgruening/augustus a repository that used to work, so I assume that is a regression.

Sorry for not being clear enough! Cheers, Bjoern

...

Hello Bjoern,

The changeset to which your link refers is the change that allows anyone that has write permission on a repository to reset all metadata on that repository from the "Repository Actions" pop-up menu on the "View repository" page. Previous to this change, this feature was restricted to the owner of the repository. I committed this changeset to the next-stble branch and merged it into the central branch, so it is available in both.

I have just double-cheked using the central branch on my local development repository, and this feature is working as expected. For example, if I have a repo owned by user test and only test has write permission on that repo, the user test1 cannot reset all metadata on the repo. However, if user test grants write permission on the repo to user test1, then user test1 can immediately reset all metadata on the repo.

Can you let me know what steps you are taking and the behavior you are seeing that differs from this?

Thanks!

Greg Von Kuster

On Oct 29, 2013, at 1:03 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

do you mean that patch?

https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc

I can reproduce that error and it is not fixed with latest galaxy-central, or did you only applied it to next-stable?

You can test with my augustus repository if you like. http://toolshed.g2.bx.psu.edu/view/bgruening/augustus

Thanks, Bjoern

...

Hello Saskia,

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has been committed to the next-stable branch and is currently running on both the test and main Galaxy tool sheds. Thanks for reporting this issue.

Greg Von Kuster

On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann s.hiltemann@erasmusmc.nl wrote:

...

I updated my Galaxies to the latest version today, and when I try to install a toolshed repository which defines an environment variable via the <set_environment> tags in the tool_dependencies.xml file, I get an error (see below).

tool_dependencies.xml:

<?xml version="1.0"?>

<tool_dependency> <set_environment version="1.0"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency>

(before the update these repositories installed without problems)

..doing the same as an action within a package dependency does still work, so for now I have just changed the tools I needed to set the environment this way, e.g.:

<tool_dependency> <package name="condel" version="1"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> Set condel environment variable </readme> </package> </tool_dependency>

Is this the preferred way of doing it, and should I change all my tools this way? or should both ways still be working?

Saskia

Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'env_var_elem' is not defined URL: http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_depende... Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response)

Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs )

Module galaxy.web.framework:229 in decorator view >> return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in manage_tool_dependencies view >> self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )

Module galaxy.web.framework:229 in decorator view >> return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in initiate_tool_dependency_installation view >> tool_dependencies=tool_dependencies )

Module tool_shed.util.common_install_util:486 in handle_tool_dependencies view >> env_var_name = env_var_elem.get( 'name', None )

NameError: global name 'env_var_elem' is not defined

---

From: S.D. Hiltemann Sent: Friday, August 02, 2013 11:19 AM To: galaxy-dev@lists.bx.psu.edu Subject: Toolshed repository update error

I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing my script to fail of course. How can I prevent this from happening?

Saskia

snippet of the code:

if [[ ! -s $rfile ]] then dummycol=${addcols:2} outputcol=${dummycol//",B."/" "} <<<<<<< local echo -e "${col_chr_name}\t${col_start_name}\t ${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile cat $rfile ======= numcommas=`echo "$addcols" | grep -o "," | wc -l` echo "numcolums: $numcommas"

  awk 'BEGIN{FS="\t";OFS="\t"}{
          if(FNR==1)
              print $0,"'"$outputcol"'";
          else{
              printf $0
              for(i=0;i<="'"$numcommas"'"+1;i++)
                  printf "\t"
              printf "\n"
          }
      }END{}' $ofile > tempofile

      mv tempofile $ofile

  return

>>>>>>> other fi

---

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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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---

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On Wed, Oct 30, 2013 at 3:58 PM, Björn Grüning bjoern.gruening@pharmazie.uni-freiburg.de wrote:

Hi John & Greg,

yes I can confirm that. Thanks for reproducing.

Btw. should I set up one test repository for every feature (lets say for ruby and R) that will stay like it is and function as test environment. Or should be write some unit tests for it?

Well if you are going to offer :).

My thoughts are this. Dave B. has built up a really nice suite of test repositories for full functional tests of various features (test/tool_shed/test_data/). Ideally R, Ruby, and Python would have functional tests - the problem with R and Ruby however is that they require a very long time to install and compile. So what I think I would ideally like to see is some sort of stub repository/script for R and Ruby that could mimic there behavior (along with corresponding stub packages). Stubs that would make sure these various environment variables are called properly and the correct arguments are passed to R and/or ruby/gem, but that will not actually compile and install these things.

That would probably be a lot of work though :), unit tests would be like my second choice for testing these features but could certainly be of great utility. Unit tests are great where they make sense and could catch some bugs for sure in these components - but it seems right now that the problems we are going to continue to encounter are many different components working together with interfaces that are changing rapidly. I feel like for such code functional tests are slightly more helpful - also this code is already functional tested frequently so they are more likely to be run by anyone pre-commit.

Short of either of these changes however, it would be wonderful to just have some static test repositories as you outlined! Perhaps making a wiki page or something with a list of these would be excellent. That could also serve as documentation examples of various features.

Any help on any of these fronts would be most appreciated Bjoern!

-John

Thanks, Bjoern

...

Thanks John,

I just sent my message as yours arrived - this will help me more quickly resolve the issue. I'll have a fix soon.

Greg Von Kuster

On Oct 30, 2013, at 4:09 PM, John Chilton chilton@msi.umn.edu wrote:

...

I can verify augustus doesn't work correctly any longer, but I do not get the same error. The package installs properly but set_environment doesn't get handled.

As far as I can tell this changeset:

https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8dcfe30fc5b92...

Would break this functionality:

<set_environment version="1.0"> <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment>

(as documented on wiki and as appears in the augustus wrappers).

In particular these three lines:

elif elem.tag == 'set_environment': env_var_name = env_var_elem.get( 'name', None ) if env_var_name:

Which have become:

elif elem.tag == 'set_environment': env_var_name = elem.get( 'name', None ) if env_var_name:

Seem problematic. It looks like the set_environment element doesn't have the name, it is the inner environment_variable elements that do. This should probably be resolved before the next release.

-John

On Wed, Oct 30, 2013 at 10:10 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

sorry for the confusion. You answered to Saskia

...

...

> This was indeed a bug (not "abut" which was a spell checker spelling > error) which has been resolved in 11116:83bed9c7dbbc. This fix has

If I search for that number I only find your fix for the repository action view. But I'm searching for the fix for ' Installing toolshed repositories with set_environment dependency'. Saskia posted that she gets that error:

NameError: global name 'env_var_elem' is not defined

And I can reproduce it with latest galaxy-central and http://toolshed.g2.bx.psu.edu/view/bgruening/augustus a repository that used to work, so I assume that is a regression.

Sorry for not being clear enough! Cheers, Bjoern

...

Hello Bjoern,

The changeset to which your link refers is the change that allows anyone that has write permission on a repository to reset all metadata on that repository from the "Repository Actions" pop-up menu on the "View repository" page. Previous to this change, this feature was restricted to the owner of the repository. I committed this changeset to the next-stble branch and merged it into the central branch, so it is available in both.

I have just double-cheked using the central branch on my local development repository, and this feature is working as expected. For example, if I have a repo owned by user test and only test has write permission on that repo, the user test1 cannot reset all metadata on the repo. However, if user test grants write permission on the repo to user test1, then user test1 can immediately reset all metadata on the repo.

Can you let me know what steps you are taking and the behavior you are seeing that differs from this?

Thanks!

Greg Von Kuster

On Oct 29, 2013, at 1:03 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

do you mean that patch?

https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc

I can reproduce that error and it is not fixed with latest galaxy-central, or did you only applied it to next-stable?

You can test with my augustus repository if you like. http://toolshed.g2.bx.psu.edu/view/bgruening/augustus

Thanks, Bjoern

> Hello Saskia, > > > This was indeed a bug (not "abut" which was a spell checker spelling > error) which has been resolved in 11116:83bed9c7dbbc. This fix has > been committed to the next-stable branch and is currently running on > both the test and main Galaxy tool sheds. Thanks for reporting this > issue. > > > Greg Von Kuster > > > > On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann > s.hiltemann@erasmusmc.nl wrote: > >> I updated my Galaxies to the latest version today, and when I try to >> install a toolshed repository which defines an environment variable >> via the <set_environment> tags in the tool_dependencies.xml file, I >> get an error (see below). >> >> tool_dependencies.xml: >> >> <?xml version="1.0"?> >> <tool_dependency> >> <set_environment version="1.0"> >> <environment_variable name="CONDEL_SCRIPT_PATH" >> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> >> </set_environment> >> </tool_dependency> >> >> (before the update these repositories installed without problems) >> >> ..doing the same as an action within a package dependency does still >> work, so for now I have just changed the tools I needed to set the >> environment this way, e.g.: >> >> <tool_dependency> >> <package name="condel" version="1"> >> <install version="1.0"> >> <actions> >> <action type="set_environment"> >> <environment_variable name="CONDEL_SCRIPT_PATH" >> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> >> </action> >> </actions> >> </install> >> <readme> >> Set condel environment variable >> </readme> >> </package> >> </tool_dependency> >> >> Is this the preferred way of doing it, and should I change all my >> tools this way? or should both ways still be working? >> >> Saskia >> >> Error Traceback: >> View as: Interactive | Text | XML (full) >> ⇝ NameError: global name 'env_var_elem' is not defined >> URL: http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_depende... >> Module weberror.evalexception.middleware:364 in respond >> view >>>> app_iter = self.application(environ, detect_start_response) >> >> Module paste.recursive:84 in __call__ view >>>> return self.application(environ, start_response) >> >> Module paste.httpexceptions:633 in __call__ view >>>> return self.application(environ, start_response) >> >> Module galaxy.web.framework.base:132 in __call__ view >>>> return self.handle_request( environ, start_response ) >> >> Module galaxy.web.framework.base:190 in handle_request view >>>> body = method( trans, **kwargs ) >> >> Module galaxy.web.framework:229 in decorator view >>>> return func( self, trans, *args, **kwargs ) >> >> Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in manage_tool_dependencies view >>>> self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) >> >> Module galaxy.web.framework:229 in decorator view >>>> return func( self, trans, *args, **kwargs ) >> >> Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in initiate_tool_dependency_installation view >>>> tool_dependencies=tool_dependencies ) >> >> Module tool_shed.util.common_install_util:486 in handle_tool_dependencies view >>>> env_var_name = env_var_elem.get( 'name', None ) >> >> NameError: global name 'env_var_elem' is not defined >> >> >> >> >> ____________________________________________________________________ >> From: S.D. Hiltemann >> Sent: Friday, August 02, 2013 11:19 AM >> To: galaxy-dev@lists.bx.psu.edu >> Subject: Toolshed repository update error >> >> >> >> I am working on putting a tool into the toolshed. I have a bash >> script wrapper. I uploaded the first version fine, but when I wanted >> to upload a revision, some unwanted characters are inserted around >> the revised function of my code (see bottom) ..the inserted "<<<<<< >> local" etc strings are causing my script to fail of course. How can >> I prevent this from happening? >> >> Saskia >> >> >> snippet of the code: >> >> >> if [[ ! -s $rfile ]] >> then >> dummycol=${addcols:2} >> outputcol=${dummycol//",B."/" "} >> <<<<<<< local >> echo -e "${col_chr_name}\t${col_start_name}\t >> ${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > >> $rfile >> cat $rfile >> ======= >> numcommas=`echo "$addcols" | grep -o "," | wc -l` >> echo "numcolums: $numcommas" >> >> awk 'BEGIN{FS="\t";OFS="\t"}{ >> if(FNR==1) >> print $0,"'"$outputcol"'"; >> else{ >> printf $0 >> for(i=0;i<="'"$numcommas"'"+1;i++) >> printf "\t" >> printf "\n" >> } >> }END{}' $ofile > tempofile >> >> mv tempofile $ofile >> >> return >>>>>>>>> other >> fi >> >> >> >> ___________________________________________________________ >> 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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On Thu, Oct 31, 2013 at 7:41 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

Hi,

...

...

Hi John & Greg,

yes I can confirm that. Thanks for reproducing.

Btw. should I set up one test repository for every feature (lets say for ruby and R) that will stay like it is and function as test environment. Or should be write some unit tests for it?

Well if you are going to offer :).

My thoughts are this. Dave B. has built up a really nice suite of test repositories for full functional tests of various features (test/tool_shed/test_data/). Ideally R, Ruby, and Python would have functional tests - the problem with R and Ruby however is that they require a very long time to install and compile. So what I think I would ideally like to see is some sort of stub repository/script for R and Ruby that could mimic there behavior (along with corresponding stub packages). Stubs that would make sure these various environment variables are called properly and the correct arguments are passed to R and/or ruby/gem, but that will not actually compile and install these things.

Is there a need to remove all repositories once they are installed? If you leave the repositories for R, Ruby, Python as long as possible installed (as far as no update comes in) you have something like a stub repository. I do not expect to change R, Ruby and Co. repositories to change frequently once the first storm is over. With a --reset-all option you could remove all of these repositories.

Hmmm... I have been thinking a lot about this. I imagine at some point the nightly tool shed tests will include options for testing install procedures - I think Peter wants this but is too afraid to come out an ask for it :). I think that combined with your test repositories below be the best way to functionally test everything.

I think the tests that are included with Galaxy are all self contained and don't have external dependencies (e.g. the source code for R or Ruby) so I still do not think this really belongs with that set of functional tests. That said if you were really passionate that these did need to be included - nose does allow conditional tests and perhaps you could implement them in such a way that they were disabled by default but could be enabled with some flag like sh run_tool_shed_functional_tests.sh --with-external-dependencies or an environment variable. It would be hard to turn down free tests :).

...

That would probably be a lot of work though :), unit tests would be like my second choice for testing these features but could certainly be of great utility. Unit tests are great where they make sense and could catch some bugs for sure in these components - but it seems right now that the problems we are going to continue to encounter are many different components working together with interfaces that are changing rapidly. I feel like for such code functional tests are slightly more helpful - also this code is already functional tested frequently so they are more likely to be run by anyone pre-commit.

Makes sense.

...

Short of either of these changes however, it would be wonderful to just have some static test repositories as you outlined! Perhaps making a wiki page or something with a list of these would be excellent. That could also serve as documentation examples of various features.

First repositories:

http://testtoolshed.g2.bx.psu.edu/view/bgruening/test_repository_setup_ruby_... http://testtoolshed.g2.bx.psu.edu/view/bgruening/test_repository_setup_r_env...

Will try to add that to the wiki soon.

Thanks so much for putting these together and for your continued contributions to the tool shed. I am really excited about the direction you are pushing things in!

-John

Thanks, Bjoern

...

Any help on any of these fronts would be most appreciated Bjoern!

-John

...

Thanks, Bjoern

...

Thanks John,

I just sent my message as yours arrived - this will help me more quickly resolve the issue. I'll have a fix soon.

Greg Von Kuster

On Oct 30, 2013, at 4:09 PM, John Chilton chilton@msi.umn.edu wrote:

...

I can verify augustus doesn't work correctly any longer, but I do not get the same error. The package installs properly but set_environment doesn't get handled.

As far as I can tell this changeset:

https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8dcfe30fc5b92...

Would break this functionality:

<set_environment version="1.0"> <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment>

(as documented on wiki and as appears in the augustus wrappers).

In particular these three lines:

elif elem.tag == 'set_environment': env_var_name = env_var_elem.get( 'name', None ) if env_var_name:

Which have become:

elif elem.tag == 'set_environment': env_var_name = elem.get( 'name', None ) if env_var_name:

Seem problematic. It looks like the set_environment element doesn't have the name, it is the inner environment_variable elements that do. This should probably be resolved before the next release.

-John

On Wed, Oct 30, 2013 at 10:10 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

sorry for the confusion. You answered to Saskia

>>> This was indeed a bug (not "abut" which was a spell checker spelling >>> error) which has been resolved in 11116:83bed9c7dbbc. This fix has

If I search for that number I only find your fix for the repository action view. But I'm searching for the fix for ' Installing toolshed repositories with set_environment dependency'. Saskia posted that she gets that error:

NameError: global name 'env_var_elem' is not defined

And I can reproduce it with latest galaxy-central and http://toolshed.g2.bx.psu.edu/view/bgruening/augustus a repository that used to work, so I assume that is a regression.

Sorry for not being clear enough! Cheers, Bjoern

> Hello Bjoern, > > The changeset to which your link refers is the change that allows anyone that has write permission on a repository to reset all metadata on that repository from the "Repository Actions" pop-up menu on the > "View repository" page. Previous to this change, this feature was restricted to the owner of the repository. I committed this changeset to the next-stble branch and merged it into the central branch, so it is available in both. > > I have just double-cheked using the central branch on my local development repository, and this feature is working as expected. For example, if I have a repo owned by user test and only test has write permission on that repo, the user test1 cannot reset all metadata on the repo. However, if user test grants write permission on the repo to user test1, then user test1 can immediately reset all metadata on the repo. > > Can you let me know what steps you are taking and the behavior you are seeing that differs from this? > > Thanks! > > Greg Von Kuster > > > On Oct 29, 2013, at 1:03 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote: > >> Hi Greg, >> >> do you mean that patch? >> >> https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc >> >> I can reproduce that error and it is not fixed with latest >> galaxy-central, or did you only applied it to next-stable? >> >> You can test with my augustus repository if you like. >> http://toolshed.g2.bx.psu.edu/view/bgruening/augustus >> >> Thanks, >> Bjoern >> >> >>> Hello Saskia, >>> >>> >>> This was indeed a bug (not "abut" which was a spell checker spelling >>> error) which has been resolved in 11116:83bed9c7dbbc. This fix has >>> been committed to the next-stable branch and is currently running on >>> both the test and main Galaxy tool sheds. Thanks for reporting this >>> issue. >>> >>> >>> Greg Von Kuster >>> >>> >>> >>> On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann >>> s.hiltemann@erasmusmc.nl wrote: >>> >>>> I updated my Galaxies to the latest version today, and when I try to >>>> install a toolshed repository which defines an environment variable >>>> via the <set_environment> tags in the tool_dependencies.xml file, I >>>> get an error (see below). >>>> >>>> tool_dependencies.xml: >>>> >>>> <?xml version="1.0"?> >>>> <tool_dependency> >>>> <set_environment version="1.0"> >>>> <environment_variable name="CONDEL_SCRIPT_PATH" >>>> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> >>>> </set_environment> >>>> </tool_dependency> >>>> >>>> (before the update these repositories installed without problems) >>>> >>>> ..doing the same as an action within a package dependency does still >>>> work, so for now I have just changed the tools I needed to set the >>>> environment this way, e.g.: >>>> >>>> <tool_dependency> >>>> <package name="condel" version="1"> >>>> <install version="1.0"> >>>> <actions> >>>> <action type="set_environment"> >>>> <environment_variable name="CONDEL_SCRIPT_PATH" >>>> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> >>>> </action> >>>> </actions> >>>> </install> >>>> <readme> >>>> Set condel environment variable >>>> </readme> >>>> </package> >>>> </tool_dependency> >>>> >>>> Is this the preferred way of doing it, and should I change all my >>>> tools this way? or should both ways still be working? >>>> >>>> Saskia >>>> >>>> Error Traceback: >>>> View as: Interactive | Text | XML (full) >>>> ⇝ NameError: global name 'env_var_elem' is not defined >>>> URL: http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_depende... >>>> Module weberror.evalexception.middleware:364 in respond >>>> view >>>>>> app_iter = self.application(environ, detect_start_response) >>>> >>>> Module paste.recursive:84 in __call__ view >>>>>> return self.application(environ, start_response) >>>> >>>> Module paste.httpexceptions:633 in __call__ view >>>>>> return self.application(environ, start_response) >>>> >>>> Module galaxy.web.framework.base:132 in __call__ view >>>>>> return self.handle_request( environ, start_response ) >>>> >>>> Module galaxy.web.framework.base:190 in handle_request view >>>>>> body = method( trans, **kwargs ) >>>> >>>> Module galaxy.web.framework:229 in decorator view >>>>>> return func( self, trans, *args, **kwargs ) >>>> >>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in manage_tool_dependencies view >>>>>> self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) >>>> >>>> Module galaxy.web.framework:229 in decorator view >>>>>> return func( self, trans, *args, **kwargs ) >>>> >>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in initiate_tool_dependency_installation view >>>>>> tool_dependencies=tool_dependencies ) >>>> >>>> Module tool_shed.util.common_install_util:486 in handle_tool_dependencies view >>>>>> env_var_name = env_var_elem.get( 'name', None ) >>>> >>>> NameError: global name 'env_var_elem' is not defined >>>> >>>> >>>> >>>> >>>> ____________________________________________________________________ >>>> From: S.D. Hiltemann >>>> Sent: Friday, August 02, 2013 11:19 AM >>>> To: galaxy-dev@lists.bx.psu.edu >>>> Subject: Toolshed repository update error >>>> >>>> >>>> >>>> I am working on putting a tool into the toolshed. I have a bash >>>> script wrapper. I uploaded the first version fine, but when I wanted >>>> to upload a revision, some unwanted characters are inserted around >>>> the revised function of my code (see bottom) ..the inserted "<<<<<< >>>> local" etc strings are causing my script to fail of course. How can >>>> I prevent this from happening? >>>> >>>> Saskia >>>> >>>> >>>> snippet of the code: >>>> >>>> >>>> if [[ ! -s $rfile ]] >>>> then >>>> dummycol=${addcols:2} >>>> outputcol=${dummycol//",B."/" "} >>>> <<<<<<< local >>>> echo -e "${col_chr_name}\t${col_start_name}\t >>>> ${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > >>>> $rfile >>>> cat $rfile >>>> ======= >>>> numcommas=`echo "$addcols" | grep -o "," | wc -l` >>>> echo "numcolums: $numcommas" >>>> >>>> awk 'BEGIN{FS="\t";OFS="\t"}{ >>>> if(FNR==1) >>>> print $0,"'"$outputcol"'"; >>>> else{ >>>> printf $0 >>>> for(i=0;i<="'"$numcommas"'"+1;i++) >>>> printf "\t" >>>> printf "\n" >>>> } >>>> }END{}' $ofile > tempofile >>>> >>>> mv tempofile $ofile >>>> >>>> return >>>>>>>>>>> other >>>> fi >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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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I know this has been needed for quite some time. I't's definitely on our near radar. I'm thinking that testing repositories of type tool_dependency_definition would cover this request since any repositories that have bot tools and a tool_dependencies.xml file are already tested. Will this be an appropriate approach to this, or am I missing something here?

Thanks!

Greg Von Kuster

On Nov 2, 2013, at 7:06 AM, Peter Cock p.j.a.cock@googlemail.com wrote:

On Fri, Nov 1, 2013 at 2:13 PM, John Chilton wrote:

...

Hmmm... I have been thinking a lot about this. I imagine at some point the nightly tool shed tests will include options for testing install procedures - I think Peter wants this but is too afraid to come out an ask for it :).

Ha ha. Am I getting to repetitive on this point? https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-pac...

Peter ___________________________________________________________ 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/

I believe this is fixed in 11184:d2b9f616e66c - at least everyting worked for me. However, committing to next-stable was a bit tweaky although I think all is ok. Please let me know if you see any problems.

Thanks!

Greg Von kuster

On Oct 30, 2013, at 4:09 PM, John Chilton chilton@msi.umn.edu wrote:

I can verify augustus doesn't work correctly any longer, but I do not get the same error. The package installs properly but set_environment doesn't get handled.

As far as I can tell this changeset:

https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8dcfe30fc5b92...

Would break this functionality:

<set_environment version="1.0"> <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment>

(as documented on wiki and as appears in the augustus wrappers).

In particular these three lines:

elif elem.tag == 'set_environment': env_var_name = env_var_elem.get( 'name', None ) if env_var_name:

Which have become:

elif elem.tag == 'set_environment': env_var_name = elem.get( 'name', None ) if env_var_name:

Seem problematic. It looks like the set_environment element doesn't have the name, it is the inner environment_variable elements that do. This should probably be resolved before the next release.

-John

On Wed, Oct 30, 2013 at 10:10 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

sorry for the confusion. You answered to Saskia

...

...

...

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has

If I search for that number I only find your fix for the repository action view. But I'm searching for the fix for ' Installing toolshed repositories with set_environment dependency'. Saskia posted that she gets that error:

NameError: global name 'env_var_elem' is not defined

And I can reproduce it with latest galaxy-central and http://toolshed.g2.bx.psu.edu/view/bgruening/augustus a repository that used to work, so I assume that is a regression.

Sorry for not being clear enough! Cheers, Bjoern

...

Hello Bjoern,

The changeset to which your link refers is the change that allows anyone that has write permission on a repository to reset all metadata on that repository from the "Repository Actions" pop-up menu on the "View repository" page. Previous to this change, this feature was restricted to the owner of the repository. I committed this changeset to the next-stble branch and merged it into the central branch, so it is available in both.

I have just double-cheked using the central branch on my local development repository, and this feature is working as expected. For example, if I have a repo owned by user test and only test has write permission on that repo, the user test1 cannot reset all metadata on the repo. However, if user test grants write permission on the repo to user test1, then user test1 can immediately reset all metadata on the repo.

Can you let me know what steps you are taking and the behavior you are seeing that differs from this?

Thanks!

Greg Von Kuster

On Oct 29, 2013, at 1:03 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

do you mean that patch?

https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc

I can reproduce that error and it is not fixed with latest galaxy-central, or did you only applied it to next-stable?

You can test with my augustus repository if you like. http://toolshed.g2.bx.psu.edu/view/bgruening/augustus

Thanks, Bjoern

...

Hello Saskia,

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has been committed to the next-stable branch and is currently running on both the test and main Galaxy tool sheds. Thanks for reporting this issue.

Greg Von Kuster

On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann s.hiltemann@erasmusmc.nl wrote:

...

I updated my Galaxies to the latest version today, and when I try to install a toolshed repository which defines an environment variable via the <set_environment> tags in the tool_dependencies.xml file, I get an error (see below).

tool_dependencies.xml:

<?xml version="1.0"?>

<tool_dependency> <set_environment version="1.0"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency>

(before the update these repositories installed without problems)

..doing the same as an action within a package dependency does still work, so for now I have just changed the tools I needed to set the environment this way, e.g.:

<tool_dependency> <package name="condel" version="1"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> Set condel environment variable </readme> </package> </tool_dependency>

Is this the preferred way of doing it, and should I change all my tools this way? or should both ways still be working?

Saskia

Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'env_var_elem' is not defined URL: http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_depende... Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response)

Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs )

Module galaxy.web.framework:229 in decorator view >> return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in manage_tool_dependencies view >> self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )

Module galaxy.web.framework:229 in decorator view >> return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in initiate_tool_dependency_installation view >> tool_dependencies=tool_dependencies )

Module tool_shed.util.common_install_util:486 in handle_tool_dependencies view >> env_var_name = env_var_elem.get( 'name', None )

NameError: global name 'env_var_elem' is not defined

---

From: S.D. Hiltemann Sent: Friday, August 02, 2013 11:19 AM To: galaxy-dev@lists.bx.psu.edu Subject: Toolshed repository update error

I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing my script to fail of course. How can I prevent this from happening?

Saskia

snippet of the code:

if [[ ! -s $rfile ]] then dummycol=${addcols:2} outputcol=${dummycol//",B."/" "} <<<<<<< local echo -e "${col_chr_name}\t${col_start_name}\t ${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile cat $rfile ======= numcommas=`echo "$addcols" | grep -o "," | wc -l` echo "numcolums: $numcommas"

 awk 'BEGIN{FS="\t";OFS="\t"}{
         if(FNR==1)
             print $0,"'"$outputcol"'";
         else{
             printf $0
             for(i=0;i<="'"$numcommas"'"+1;i++)
                 printf "\t"
             printf "\n"
         }
     }END{}' $ofile > tempofile

     mv tempofile $ofile

 return

>>>>>>> other fi

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Hello Bjoern,

Can you confirm that you have the following status for your tool dependencies when you attempt to install your augustus repository from the main tool shed? I haven't tracked down the reason that the AUGUSTUS_SCRIPT_PATH dependency is in the Never installed state. Is this dependecny the one where you've seen this problem?

Thabnks,

Greg Von kuster

Tool shed repository 'augustus' tool dependencies

Name Version Type Status Error AUGUSTUS_SCRIPT_PATH None set_environment Never installed augustus 2.7 package Installed

On Oct 30, 2013, at 11:10 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

Hi Greg,

sorry for the confusion. You answered to Saskia

...

...

...

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has

If I search for that number I only find your fix for the repository action view. But I'm searching for the fix for ' Installing toolshed repositories with set_environment dependency'. Saskia posted that she gets that error:

NameError: global name 'env_var_elem' is not defined

And I can reproduce it with latest galaxy-central and http://toolshed.g2.bx.psu.edu/view/bgruening/augustus a repository that used to work, so I assume that is a regression.

Sorry for not being clear enough! Cheers, Bjoern

...

Hello Bjoern,

The changeset to which your link refers is the change that allows anyone that has write permission on a repository to reset all metadata on that repository from the "Repository Actions" pop-up menu on the "View repository" page. Previous to this change, this feature was restricted to the owner of the repository. I committed this changeset to the next-stble branch and merged it into the central branch, so it is available in both.

I have just double-cheked using the central branch on my local development repository, and this feature is working as expected. For example, if I have a repo owned by user test and only test has write permission on that repo, the user test1 cannot reset all metadata on the repo. However, if user test grants write permission on the repo to user test1, then user test1 can immediately reset all metadata on the repo.

Can you let me know what steps you are taking and the behavior you are seeing that differs from this?

Thanks!

Greg Von Kuster

On Oct 29, 2013, at 1:03 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote:

...

Hi Greg,

do you mean that patch?

https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc

I can reproduce that error and it is not fixed with latest galaxy-central, or did you only applied it to next-stable?

You can test with my augustus repository if you like. http://toolshed.g2.bx.psu.edu/view/bgruening/augustus

Thanks, Bjoern

...

Hello Saskia,

This was indeed a bug (not "abut" which was a spell checker spelling error) which has been resolved in 11116:83bed9c7dbbc. This fix has been committed to the next-stable branch and is currently running on both the test and main Galaxy tool sheds. Thanks for reporting this issue.

Greg Von Kuster

On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann s.hiltemann@erasmusmc.nl wrote:

...

I updated my Galaxies to the latest version today, and when I try to install a toolshed repository which defines an environment variable via the <set_environment> tags in the tool_dependencies.xml file, I get an error (see below).

tool_dependencies.xml:

<?xml version="1.0"?>

<tool_dependency> <set_environment version="1.0"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency>

(before the update these repositories installed without problems)

..doing the same as an action within a package dependency does still work, so for now I have just changed the tools I needed to set the environment this way, e.g.:

<tool_dependency> <package name="condel" version="1"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="CONDEL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> Set condel environment variable </readme> </package> </tool_dependency>

Is this the preferred way of doing it, and should I change all my tools this way? or should both ways still be working?

Saskia

Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'env_var_elem' is not defined URL: http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_depende... Module weberror.evalexception.middleware:364 in respond view

...

> app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__ view

...

> return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__ view

...

> return self.application(environ, start_response)

Module galaxy.web.framework.base:132 in __call__ view

...

> return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:190 in handle_request view

...

> body = method( trans, **kwargs )

Module galaxy.web.framework:229 in decorator view

...

> return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in manage_tool_dependencies view

...

> self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )

Module galaxy.web.framework:229 in decorator view

...

> return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in initiate_tool_dependency_installation view

...

> tool_dependencies=tool_dependencies )

Module tool_shed.util.common_install_util:486 in handle_tool_dependencies view

...

> env_var_name = env_var_elem.get( 'name', None )

NameError: global name 'env_var_elem' is not defined

---

From: S.D. Hiltemann Sent: Friday, August 02, 2013 11:19 AM To: galaxy-dev@lists.bx.psu.edu Subject: Toolshed repository update error

I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing my script to fail of course. How can I prevent this from happening?

Saskia

snippet of the code:

if [[ ! -s $rfile ]] then dummycol=${addcols:2} outputcol=${dummycol//",B."/" "} <<<<<<< local echo -e "${col_chr_name}\t${col_start_name}\t ${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile cat $rfile ======= numcommas=`echo "$addcols" | grep -o "," | wc -l` echo "numcolums: $numcommas"

  awk 'BEGIN{FS="\t";OFS="\t"}{
          if(FNR==1)
              print $0,"'"$outputcol"'"; 
          else{
              printf $0
              for(i=0;i<="'"$numcommas"'"+1;i++)
                  printf "\t"
              printf "\n"
          }
      }END{}' $ofile > tempofile

      mv tempofile $ofile

  return

...

>>>>>> other

fi

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---

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---

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