On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> On Feb 3, 2014, at 7:01 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>>>
>>> Returning to the MIRA4 problem, I got a meaningful test
>>> failure which I fixed (I hadn't set an environment variable
>>> in the install script), but I now get only partial test output:
>>>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
>>> ...
>>>
>>> That's all fine, but where are the test results for mira_bait which
>>> I would expect to pass?
>>>
>>
>> It looks lie the mira_bait tests results are being populated, but
>> the tests are failing, not passing. This doesn't look like an
>> issue with the Tool Shed's install and test framework.
>
> Confirmed - the Tool Shed issue where only partial test output
> was shown is fixed (did you work out why the test output was
> missing?).
>
> I was hoping to see a passing test, but I can now see a failing
> test (still something not quite right with my dependency
> installation script - I'll look at this next week hopefully).
Hi Greg,
I added a little more debug information to the mirabait test,
which confirms a problem in the tool_dependencies.xml file:
Missing mirabait under $MIRA4,
'/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/mirabait'
Folder contained: env.sh
i.e. $MIRA4 was set to $INSTALL_DIR which is the folder
/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/
and (surprisingly) it only contains one file, env.sh
Greg: Could you confirm that on the server? i.e. what does this give?
$ ls -l /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/
...
Upon downloading mira_4.0_linux-gnu_x86_64_static.tar.bz2
and decompressing it, the tool shed should have changed into
the main folder mira_4.0_linux-gnu_x86_64_static and then
moved the contents of the bin folder into the $INSTALL_DIR,
<action
type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2</action>
<action type="move_directory_files">
<source_directory>bin</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
i.e. Move files mira, mirabait, miraconvert and miramem
into $INSTALL_DIR
I am somewhat puzzled - other tools like the BLAST+
installers use a very similar setup and work fine (although
there I used $PATH instead).
Thanks,
Peter
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