Question: Toolshed tool not available ( package_cairo_1_12_14 )
gravatar for matthias.desmet
3.0 years ago by
matthias.desmet150 wrote:


I'm trying to install a tool from the public toolshed into my local galaxy instance. However, the installation process stops with the following error:

tool_shed.galaxy_install.install_manager ERROR 2015-12-17 10:53:13,855 No content returned from tool shed repository version request to
tool_shed.galaxy_install.install_manager ERROR 2015-12-17 10:53:15,162 Error installing tool dependency pixman version 0.32.4: coercing to Unicode: need string or buffer, NoneType found
Traceback (most recent call last):
  File "lib/tool_shed/galaxy_install/", line 203, in install_specified_tool_dependencies
    from_tool_migration_manager=from_tool_migration_manager )
  File "lib/tool_shed/galaxy_install/", line 306, in install_package
    tool_dependency_db_records=None )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 97, in process_tag_set
    tool_dependency_db_records=tool_dependency_db_records )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 519, in process_tag_set
    from_tool_migration_manager=from_tool_migration_manager )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 471, in handle_complex_repository_dependency_for_package
    tool_dependencies_config = suc.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
  File "lib/tool_shed/util/", line 206, in get_absolute_path_to_file_in_repository
    for root, dirs, files in os.walk( repo_files_dir ):
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/", line 276, in walk
    names = listdir(top)
TypeError: coercing to Unicode: need string or buffer, NoneType found


and all the subsequent tool dependecies also fail to install with the same 'TypeError'

Seems like the tool is no longer available in the repository?

(Galaxy v15.10 - Ubuntu 14.04.03 LTS)


toolshed galaxy • 812 views
ADD COMMENTlink modified 3.0 years ago by Bjoern Gruening5.1k • written 3.0 years ago by matthias.desmet150
gravatar for Bjoern Gruening
3.0 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

Hi Matthias,

the tool is there, the problem is that pixman is not correctly installing for you. Can you try to install this special repository and maybe the pixman 0.32.6 as well and tell us if you see any specific error message?



ADD COMMENTlink written 3.0 years ago by Bjoern Gruening5.1k

Hi Björn,

First of all, a very happy new year! Sorry it took so long for me to reply, but I had some vacation planned during the holidays.
Indeed, installing both pixman and freetype separately seems to have fixed the issue. It seems there is an issue with the dependency handling when installing a tool.

Anyway, it's fixed now, so thank you very much!

PS: any idea where the TypeError comes from? I'm keep on getting the same error message when installing different tools. Could it be an issue with Python?


ADD REPLYlink written 2.9 years ago by matthias.desmet150

I guess this is more an issue of the encoding of your database. Can you enable UTF-8 encoding?

ADD REPLYlink written 2.8 years ago by Bjoern Gruening5.1k
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