Problem with 'galaxy_packages' dependency resolver in versionless mode
Dear developers I'm having problems trying to use the 'galaxy_packages' dependency resolver in versionless mode, as described in the docs at: https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html#gal... As I understand this: if I manually create a directory structure of the form e.g. /path/to/local_tool_dependencies/my_package/default/ which contains an env.sh file, and if my dependency_resolvers_conf.xml file includes the line: <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" /> then at run time Galaxy should be able to resolve the following requirement in a tool XML file: <requirement type="package">my_package</requirement> Unfortunately although the "versioned" galaxy_packages resolver works as expected (when placed ahead of the "versionless" resolver), I don't seem able to get this working with Galaxy v16.10. Can anyone point out what I'm doing wrong? Thanks! Best wishes Peter -- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hi Peter, can you try to make /path/to/local_tool_dependencies/my_package/default a symlink? Ciao, Bjoern Am 20.01.2017 um 16:41 schrieb Peter Briggs:
Dear developers
I'm having problems trying to use the 'galaxy_packages' dependency resolver in versionless mode, as described in the docs at:
https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html#gal...
As I understand this: if I manually create a directory structure of the form e.g. /path/to/local_tool_dependencies/my_package/default/ which contains an env.sh file, and if my dependency_resolvers_conf.xml file includes the line:
<galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
then at run time Galaxy should be able to resolve the following requirement in a tool XML file:
<requirement type="package">my_package</requirement>
Unfortunately although the "versioned" galaxy_packages resolver works as expected (when placed ahead of the "versionless" resolver), I don't seem able to get this working with Galaxy v16.10.
Can anyone point out what I'm doing wrong?
Thanks!
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Hello Bjoern Yes it looks like making the 'default' directory into a symlink makes this work. Thanks for your help and sorry not to get back to you sooner! Best wishes Peter On 20/01/17 16:56, Björn Grüning wrote:
Hi Peter,
can you try to make /path/to/local_tool_dependencies/my_package/default a symlink?
Ciao, Bjoern
Am 20.01.2017 um 16:41 schrieb Peter Briggs:
Dear developers
I'm having problems trying to use the 'galaxy_packages' dependency resolver in versionless mode, as described in the docs at:
https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html#gal...
As I understand this: if I manually create a directory structure of the form e.g. /path/to/local_tool_dependencies/my_package/default/ which contains an env.sh file, and if my dependency_resolvers_conf.xml file includes the line:
<galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
then at run time Galaxy should be able to resolve the following requirement in a tool XML file:
<requirement type="package">my_package</requirement>
Unfortunately although the "versioned" galaxy_packages resolver works as expected (when placed ahead of the "versionless" resolver), I don't seem able to get this working with Galaxy v16.10.
Can anyone point out what I'm doing wrong?
Thanks!
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
I recently reworked the dependency resolver documentation and made this explicit. I don't think the previous revision of that document mentioned this important caveat at all. Thanks for Galaxy-ing! Thanks, -John On Tue, Jan 24, 2017 at 7:01 AM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
Hello Bjoern
Yes it looks like making the 'default' directory into a symlink makes this work.
Thanks for your help and sorry not to get back to you sooner!
Best wishes
Peter
On 20/01/17 16:56, Björn Grüning wrote:
Hi Peter,
can you try to make /path/to/local_tool_dependencies/my_package/default a symlink?
Ciao, Bjoern
Am 20.01.2017 um 16:41 schrieb Peter Briggs:
Dear developers
I'm having problems trying to use the 'galaxy_packages' dependency resolver in versionless mode, as described in the docs at:
https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html#gal...
As I understand this: if I manually create a directory structure of the form e.g. /path/to/local_tool_dependencies/my_package/default/ which contains an env.sh file, and if my dependency_resolvers_conf.xml file includes the line:
<galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" />
then at run time Galaxy should be able to resolve the following requirement in a tool XML file:
<requirement type="package">my_package</requirement>
Unfortunately although the "versioned" galaxy_packages resolver works as expected (when placed ahead of the "versionless" resolver), I don't seem able to get this working with Galaxy v16.10.
Can anyone point out what I'm doing wrong?
Thanks!
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Björn Grüning -
John Chilton -
Peter Briggs