attempt to fix issue #27

annefou commented 5 years ago

I am trying to use climate.usegalaxy.eu and psy-maps fails because it attempts to write in /opt/galaxy (that is readonly). I am hoping that redefining HOME environment variable would help but I am not sure...

@bgruening Do you think that would solve issue #27 ?

bgruening commented 5 years ago

Yes it would, but I commented on the issue a better fix. I already applied that fix already to usealaxy.eu, so please try this tool again.

I need to change a train soon, so might not be available the next 12h :( But will catch up tomorrow.

annefou commented 5 years ago

Yes it works!!!

Thank you so much!

bgruening commented 5 years ago

@annefou do I need to do here something? Sorry, this slipped through ...

annefou commented 5 years ago

I don't know if we have to do anything; now it works on the Galaxy climate instance. Do you have "local" changes that are not reported in the master branch?

bgruening commented 5 years ago

Yes :)

<tool id="cds_essential_variability" name="Copernicus Essential Climate Variables" version="0.1.4">
    <description>for assessing climate variability</description>
    <requirements>
        <requirement type="package" version="3">python</requirement>
        <requirement type="package" version="0.1.4">cdsapi</requirement>
        <requirement type="package" version="1.9.6">cdo</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       HOME=`pwd`  &&
       cp \$COPERNICUS_CDSAPIRC_KEY_FILE .cdsapirc | true &&
       python3 '$__tool_directory__/ecv_retrieve.py'
            'ecv-for-climate-change' '$variable'
            --month '$month'
        #if str($product_type.product) == 'monthly_mean'
            --year '$product_type.year'
            --time_aggregation '1_month'
        #else if str($product_type.product) == 'anomaly'
            --time_aggregation '$product_type.selector'
            --year '$product_type.year'
        #else
            --year '2018'
           --time_aggregation '1_month'
        #end if
           --product_type '$product_type.product'
           --format 'tgz' --output 'tmp.tgz'
           --verbose                                       &&
           tar zxvf tmp.tgz                                &&
           cat *.grib > tmpg.grib                          &&
           cdo remapcon,$adv.resol -setgridtype,regular tmpg.grib tmp.grib &&
           cdo -f nc -t ecmwf copy tmp.grib tmp.nc
    ]]></command>

annefou commented 5 years ago

Ok. But this PR was for psy-maps.xml not essential_climate_variables.xml so I am not sure I fully understand.

annefou commented 5 years ago

I close this issue. We will soon have a newer version of this tool (with new parameters, etc.) (I will make a new pull request soon).

NordicESMhub / galaxy-tools

attempt to fix issue #27 #28