On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>> Peter,
>>
>> I did some investigating, and it turns out that the if [[ condition ]]
>> syntax used in the ncbi tool dependency is only compatible with bash, not
>> sh.
>
> Does that mean the test system has switched between sh and bash
> and back to sh again?

Is there anything written down about the expected shell(s)
available for a standard Galaxy instance?

>> For sh, the corresponding syntax would look like:
>>
>> if [ "$string" = "value" ]
>> then
>>     echo "string is equal to value"
>> fi
>>
>> However, it strikes me that the platform detection and download url
>> determination could also be done using the recently introduced
>> <actions_group> feature, which would bypass shell-dependent
>> conditional syntax entirely.
>
> Yes, but is that in stable releases for galaxy-dist yet?

In the meantime I will try that on the Test Tool Shed, based
on the tool_dependencies.xml example you shared before:

http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26/c83440a9bdfb

Note there seems to me to be a lot of duplication - I would like
a way to unambiguously combine multiple CPU architectures
into a single action.

For example, combine these:

<actions os="darwin" architecture="x86_64">
<actions os="darwin" architecture="i386">

into:

<actions os="darwin" architecture="x86_64,i386">

or just:

<actions os="darwin">

and similarly, combine these:

<actions os="linux" architecture="i386">
<actions os="linux" architecture="i686">

into something like:

<actions os="linux" architecture="i386,i686">

Assuming that works on the Test Tool Shed, and the code for
this is already in the stable releases, I will update the main
Tool Shed definition as well.

Thanks,

Peter
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