Wiki documentation for tool_dependencies.xml file
Hi all, Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g. https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies What I am looking for is something like the wiki page for the tool XML: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax This missing page should do things like list all the XML tags, for example showing all the permitted actions in tool_dependencies.xml? What are the pre-defined environment variables like $INSTALL_DIR, and my specific question today - does that have a trailing slash or not? Peter
Hi Peter, the page you are looking for is: https://wiki.galaxyproject.org/ToolDependenciesTagSets I think it should be better linked, I had to bookmark it! Cheers, Nicola Il 02.09.2015 12:33 Peter Cock ha scritto:
Hi all,
Is there a page on the wiki describing the tool_dependencies.xml file syntax?
Searching finds pages with examples, e.g.
https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository [1]
https://wiki.galaxyproject.org/ComplexRepositoryDependencies [2]
What I am looking for is something like the wiki page for the tool XML: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax [3]
This missing page should do things like list all the XML tags, for example showing all the permitted actions in tool_dependencies.xml?
What are the pre-defined environment variables like $INSTALL_DIR,
and my specific question today - does that have a trailing slash or not?
Peter
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Lovely, thanks! I've added a couple of links pointing to that page :) It does list a few of relevant environment variables, $INSTALL_DIR, $REPOSITORY_INSTALL_DIR and $TMP_WORK_DIR, but does not comment on if these directory names include a trailing slash or not... Peter On Wed, Sep 2, 2015 at 12:12 PM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Hi Peter, the page you are looking for is:
https://wiki.galaxyproject.org/ToolDependenciesTagSets
I think it should be better linked, I had to bookmark it!
Cheers, Nicola
Il 02.09.2015 12:33 Peter Cock ha scritto:
Hi all,
Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g.
https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies
What I am looking for is something like the wiki page for the tool XML: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
This missing page should do things like list all the XML tags, for example showing all the permitted actions in tool_dependencies.xml?
What are the pre-defined environment variables like $INSTALL_DIR, and my specific question today - does that have a trailing slash or not?
Peter
Hi Peter, it looks like they are without the trailing slash: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/galaxy_instal... https://github.com/galaxyproject/galaxy/pull/511/files#diff-93a0802a2778786e... Ciao, Bjoern On 02.09.2015 13:29, Peter Cock wrote:
Lovely, thanks! I've added a couple of links pointing to that page :)
It does list a few of relevant environment variables, $INSTALL_DIR, $REPOSITORY_INSTALL_DIR and $TMP_WORK_DIR, but does not comment on if these directory names include a trailing slash or not...
Peter
On Wed, Sep 2, 2015 at 12:12 PM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Hi Peter, the page you are looking for is:
https://wiki.galaxyproject.org/ToolDependenciesTagSets
I think it should be better linked, I had to bookmark it!
Cheers, Nicola
Il 02.09.2015 12:33 Peter Cock ha scritto:
Hi all,
Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g.
https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies
What I am looking for is something like the wiki page for the tool XML: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
This missing page should do things like list all the XML tags, for example showing all the permitted actions in tool_dependencies.xml?
What are the pre-defined environment variables like $INSTALL_DIR, and my specific question today - does that have a trailing slash or not?
Peter
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/
Thanks Bjoern, Yes, reading the code in that file all three do look to be created via os.path.abspath(...) and so won't have a trailing slash. I've added that information to the wiki. I'm assuming this now in my MIRA 4.9.5 package, but a double trailing slash should be harmless anyway: https://github.com/peterjc/pico_galaxy/commit/708050c2bd6e7e11eee53bfeaee6ff... Right now I am assuming the trailing slash when doing ${MIRA4_9}mirabait which I want to default to using mirabait on the $PATH if the variable $MIRA4_9 is not setup. Peter On Wed, Sep 2, 2015 at 2:08 PM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Peter,
it looks like they are without the trailing slash:
https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/galaxy_instal... https://github.com/galaxyproject/galaxy/pull/511/files#diff-93a0802a2778786e...
Ciao, Bjoern
On 02.09.2015 13:29, Peter Cock wrote:
Lovely, thanks! I've added a couple of links pointing to that page :)
It does list a few of relevant environment variables, $INSTALL_DIR, $REPOSITORY_INSTALL_DIR and $TMP_WORK_DIR, but does not comment on if these directory names include a trailing slash or not...
Peter
On Wed, Sep 2, 2015 at 12:12 PM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Hi Peter, the page you are looking for is:
https://wiki.galaxyproject.org/ToolDependenciesTagSets
I think it should be better linked, I had to bookmark it!
Cheers, Nicola
Il 02.09.2015 12:33 Peter Cock ha scritto:
Hi all,
Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g.
https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies
What I am looking for is something like the wiki page for the tool XML: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
This missing page should do things like list all the XML tags, for example showing all the permitted actions in tool_dependencies.xml?
What are the pre-defined environment variables like $INSTALL_DIR, and my specific question today - does that have a trailing slash or not?
Peter
___________________________________________________________ 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/
Tricky, thanks for updating the wiki! On 02.09.2015 15:23, Peter Cock wrote:
Thanks Bjoern,
Yes, reading the code in that file all three do look to be created via os.path.abspath(...) and so won't have a trailing slash. I've added that information to the wiki.
I'm assuming this now in my MIRA 4.9.5 package, but a double trailing slash should be harmless anyway:
https://github.com/peterjc/pico_galaxy/commit/708050c2bd6e7e11eee53bfeaee6ff...
Right now I am assuming the trailing slash when doing ${MIRA4_9}mirabait which I want to default to using mirabait on the $PATH if the variable $MIRA4_9 is not setup.
Peter
On Wed, Sep 2, 2015 at 2:08 PM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Peter,
it looks like they are without the trailing slash:
https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/galaxy_instal... https://github.com/galaxyproject/galaxy/pull/511/files#diff-93a0802a2778786e...
Ciao, Bjoern
On 02.09.2015 13:29, Peter Cock wrote:
Lovely, thanks! I've added a couple of links pointing to that page :)
It does list a few of relevant environment variables, $INSTALL_DIR, $REPOSITORY_INSTALL_DIR and $TMP_WORK_DIR, but does not comment on if these directory names include a trailing slash or not...
Peter
On Wed, Sep 2, 2015 at 12:12 PM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Hi Peter, the page you are looking for is:
https://wiki.galaxyproject.org/ToolDependenciesTagSets
I think it should be better linked, I had to bookmark it!
Cheers, Nicola
Il 02.09.2015 12:33 Peter Cock ha scritto:
Hi all,
Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g.
https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies
What I am looking for is something like the wiki page for the tool XML: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
This missing page should do things like list all the XML tags, for example showing all the permitted actions in tool_dependencies.xml?
What are the pre-defined environment variables like $INSTALL_DIR, and my specific question today - does that have a trailing slash or not?
Peter
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)
-
Bjoern Gruening -
Nicola Soranzo -
Peter Cock