Hi again,

I have been able to solve this problems thanks to fix commited by nsoranzo
and I installed the package_trinity_2_1_1 correclty. However, when
installing trinity (e4a9e0798360) there is a problem with the edger and
express dependencies. In the trinity's tool_dependencies.xml file these two
packages appear as:

<package name="edger" version="3.12.0">
<package name="express" version="1.5.1">

However, in the tool_dependencies.xml file from these packages they appear
with a different name:

<package name="bioconductor-edger" version="3.12.0">
<package name="eXpress" version="1.5.1">

Therefore, I suppose that Galaxy does not recognize them and they are shown
as Never Installed.

Could you look into this?

Regards,
Jose


2016-06-09 17:09 GMT+02:00 Jose Juan Almagro Armenteros <jjalmagro@gmail.com

:

Hello,

I am having troubles installing the last version of the tool Trinity. I
found that I have the same error as this issue (
https://github.com/galaxyproject/galaxy/issues/1947), so I tried the
suggested solution. It didn't work, so I posted the error in the issue.

Then, I tried to change the tmp folder to another one in the same
filesytem (and undoing the previous solution).  Again it didn't work, but
it gave a different error:


File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 123, in install_and_build_package_via_fabric

    tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict )

  File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 108, in install_and_build_package
    initial_download=False )

  File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step
    initial_download=initial_download )

  File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 845, in execute_step

    destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) )

  File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 864, in move_directory_files
    shutil.move( source_file, destination_file )
  File "/usr/lib/python2.7/shutil.py", line 130, in copy2
    copyfile(src, dst)
  File "/usr/lib/python2.7/shutil.py", line 82, in copyfile
    with open(src, 'rb') as fsrc:


[Errno 21] Is a directory: '/steno-internal/projects/galaxy/galaxy-dist/tmp/tmp-toolshed-mtd8Exq2w/trinityrnaseq-2.1.1/trinity-plugins/jellyfish'

I am using the Galaxy release *16.01. *Do you know how could I solve this
problem?

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