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
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