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_dependencies?repository_id=b847e822bdc195d0&operation=install
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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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
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/