Toolshed : tool_dependency xml, action problem

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Toolshed : tool_dependency xml, action problem

Nicolas Lapalu
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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Re: Toolshed : tool_dependency xml, action problem

Kandalaft, Iyad
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  [hidden email]
Telephone | Téléphone 613-759-1228
Facsimile | Télécopieur 613-759-1701
Teletypewriter | Téléimprimeur 613-773-2600
Government of Canada | Gouvernement du Canada



-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Nicolas Lapalu
Sent: Monday, July 07, 2014 5:57 AM
To: [hidden email]
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/

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in your mail client.  To manage your subscriptions to this
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Re: Toolshed : tool_dependency xml, action problem

Nicolas Lapalu
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  [hidden email]
> Telephone | Téléphone 613-759-1228
> Facsimile | Télécopieur 613-759-1701
> Teletypewriter | Téléimprimeur 613-773-2600
> Government of Canada | Gouvernement du Canada
>
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Nicolas Lapalu
> Sent: Monday, July 07, 2014 5:57 AM
> To: [hidden email]
> 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:
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Re: Toolshed : tool_dependency xml, action problem

Greg Von Kuster
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 <[hidden email]> 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  [hidden email]
>> Telephone | Téléphone 613-759-1228
>> Facsimile | Télécopieur 613-759-1701
>> Teletypewriter | Téléimprimeur 613-773-2600
>> Government of Canada | Gouvernement du Canada
>>
>>
>>
>> -----Original Message-----
>> From: [hidden email] [mailto:[hidden email]] On Behalf Of Nicolas Lapalu
>> Sent: Monday, July 07, 2014 5:57 AM
>> To: [hidden email]
>> 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:
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Re: Toolshed : tool_dependency xml, action problem

Nicolas Lapalu
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 <[hidden email]> 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  [hidden email]
>>> Telephone | Téléphone 613-759-1228
>>> Facsimile | Télécopieur 613-759-1701
>>> Teletypewriter | Téléimprimeur 613-773-2600
>>> Government of Canada | Gouvernement du Canada
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: [hidden email] [mailto:[hidden email]] On Behalf Of Nicolas Lapalu
>>> Sent: Monday, July 07, 2014 5:57 AM
>>> To: [hidden email]
>>> 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:
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Re: Toolshed : tool_dependency xml, action problem

Greg Von Kuster
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 <[hidden email]> 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 <[hidden email]> 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  [hidden email]
>>>> Telephone | Téléphone 613-759-1228
>>>> Facsimile | Télécopieur 613-759-1701
>>>> Teletypewriter | Téléimprimeur 613-773-2600
>>>> Government of Canada | Gouvernement du Canada
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: [hidden email] [mailto:[hidden email]] On Behalf Of Nicolas Lapalu
>>>> Sent: Monday, July 07, 2014 5:57 AM
>>>> To: [hidden email]
>>>> 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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