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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