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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___________________________________________________________
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and other Galaxy lists, please use the interface at:
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