Question: python_mysqldb and R depenedencies missing after installation
gravatar for Mic
3.3 years ago by
Mic70 wrote:

I installed ceas (Owner:pjbriggs, Revision:f411ce97a351), but I have got problems with the following "Installed, missing tool dependencies":

R 3.1.2

configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: error: --with-readline=yes (default) and headers/libs are not available

python_mysqldb 1.2.5

File "/galaxy-central/lib/tool_shed/galaxy_install/", line 142, in install_and_build_package_via_fabric
    tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict )
  File "/galaxy-central/lib/tool_shed/galaxy_install/", line 100, in install_and_build_package
    initial_download=True )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 32, in execute_step
    initial_download=initial_download )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 685, in execute_step
    dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 223, in url_download
    extraction_path = archive.extract( install_dir )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 89, in extract
    os.chmod( absolute_filepath, unix_permissions )

[Errno 2] No such file or directory: '/export/galaxy-central/database/files/tmp-toolshed-mtdk8TtAR/MySQL-python-1.2.5/MySQL-python-1.2.5/GPL-2.0'

How is it possible to fix it?

Thank you in advance.


ceas galaxy docker • 783 views
ADD COMMENTlink written 3.3 years ago by Mic70

Which OS are you on? Is this OS-X?

ADD REPLYlink written 3.3 years ago by Bjoern Gruening5.1k

I was creating a docker image based on bgruening/galaxy-stable:dev. Docker 1.7.1 is running on CentOS 6.6.

ADD REPLYlink written 3.3 years ago by Mic70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 177 users visited in the last hour