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
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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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