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.Kandalaft@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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/

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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.lapalu@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.Kandalaft@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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/

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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.lapalu@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.lapalu@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.Kandalaft@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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/