I wasn't aware of a scenario where the value of dir could be None, so thanks 
for pointing this out.  It should be fixed in 14088:23f0c41b1cd7

Greg Von Kuster

On Jul 17, 2014, at 8:15 AM, Nicolas Lapalu <nicolas.lap...@versailles.inra.fr> 
wrote:

> Hi Greg,
> 
> not in the current, in version "2014-05-14", but I think the bug is still 
> there.
> 
> current version :
> 
> 83                    for action_tup in filtered_actions:
> 84                        current_dir = os.path.abspath( os.path.join( 
> work_dir, dir ) )
> 
> Fix:
> 
> 83                    for action_tup in filtered_actions:
> ..                          if dir is None:
>                               dir = ''
> 84                        current_dir = os.path.abspath( os.path.join( 
> work_dir, dir ) )
> 
> +
> nico
> 
> 
> Le 15/07/2014 20:41, Greg Von Kuster a écrit :
>> Are the problems described in this thread occurring with the latest Galaxy 
>> release?  The references to the code lines do not seem to reflect the latest 
>> Galaxy release.
>> 
>> Thanks,
>> 
>> Greg Von Kuster
>> 
>> On Jul 7, 2014, at 10:34 AM, Nicolas Lapalu 
>> <nicolas.lap...@versailles.inra.fr> wrote:
>> 
>>> Hi
>>> 
>>> There's a bug in the 
>>> "galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py" file.
>>> line 79 : dir can be equal to None, but os.path.join() raises an error with 
>>> an arg equal to None
>>> To fix it :
>>> if dir == None:
>>>    dir = ''
>>> 
>>> nico
>>> 
>>> Le 07/07/2014 14:38, Kandalaft, Iyad a écrit :
>>>> That error sounds like it's trying to merge the current working directory 
>>>> with the path supplied in the "CHMOD" tag.
>>>>      current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) <-- 
>>>> join work_dir with dir
>>>> 
>>>> You have 2 possibilities to try:
>>>> 1. Eliminate the $INSTALLDIR from the path in the XML if you're already in 
>>>> that path
>>>> 2. Changedir to the path before trying the CHMOD tag and use "." as the 
>>>> path
>>>> 
>>>> 
>>>> Iyad Kandalaft
>>>> Microbial Biodiversity Bioinformatics
>>>> Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
>>>> 960 Carling Ave.| 960 Ave. Carling
>>>> Ottawa, ON| Ottawa (ON) K1A 0C6
>>>> E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca
>>>> Telephone | Téléphone 613-759-1228
>>>> Facsimile | Télécopieur 613-759-1701
>>>> Teletypewriter | Téléimprimeur 613-773-2600
>>>> Government of Canada | Gouvernement du Canada
>>>> 
>>>> 
>>>> 
>>>> -----Original Message-----
>>>> From: galaxy-dev-boun...@lists.bx.psu.edu 
>>>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nicolas Lapalu
>>>> Sent: Monday, July 07, 2014 5:57 AM
>>>> To: galaxy-dev@lists.bx.psu.edu
>>>> Subject: [galaxy-dev] Toolshed : tool_dependency xml, action problem
>>>> 
>>>> Hi all,
>>>> 
>>>> I'm trying to package my tool wrapper to release it in the ToolShed. I 
>>>> need to download the associated binary file and change the permissions.
>>>> I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
>>>> My tool_dependency_dir is well defined in my universe file. The download 
>>>> is ok, but I get an error during the "chmod" action.
>>>> So I tried with your example, faToTwoBit 
>>>> (https://wiki.galaxyproject.org/DownloadingBinaries), and I get the same 
>>>> bug. Do you know the problem ? Do I need to configure someting else ?
>>>> 
>>>> log :
>>>> 
>>>> tool_shed.util.tool_dependency_util DEBUG 2014-07-07 11:28:34,346 Updating 
>>>> an existing record for version 0.0.1 of tool dependency faToTwoBit for 
>>>> revision 5ac8ed26842c of repository mytool by updating the status from 
>>>> Never installed to Installing.
>>>> tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG
>>>> 2014-07-07 11:28:34,374 Attempting to download from 
>>>> http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit to bin
>>>> 127.0.0.1 - - [07/Jul/2014:11:28:36 +0200] "POST 
>>>> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - 
>>>> "http://127.0.0.1:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
>>>> (X11; Linux x86_64; rv:24.0) Gecko/20140610 Firefox/24.0 Iceweasel/24.6.0"
>>>> tool_shed.galaxy_install.install_manager ERROR 2014-07-07 11:28:39,038 
>>>> Error installing tool dependency faToTwoBit version 0.0.1.
>>>> Traceback (most recent call last):
>>>>    File
>>>> "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>>>> line 110, in install_and_build_package_via_fabric
>>>>      tool_dependency = self.install_and_build_package( app, 
>>>> tool_shed_repository, tool_dependency, actions_dict )
>>>>    File
>>>> "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>>>> line 79, in install_and_build_package
>>>>      current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
>>>>    File "/usr/lib/python2.7/posixpath.py", line 75, in join
>>>>      if b.startswith('/'):
>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>> 
>>>> Thanks for your help;
>>>> nico
>>>> ___________________________________________________________
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> 
> ___________________________________________________________
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