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 >> ___________________________________________________________ >> 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/ > > ___________________________________________________________ > 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/ > ___________________________________________________________ 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/
