So 'binary' and 'python-module' module are currently just treated differently from 'package' in this context because they are kind of not in use? But isn't it then a good idea to also include these type tags into the dependency management system by generally changing this line to:

if requirement.type in [ 'package', 'set_environment', 'binary', 'python-module']

or just kick out the whole if clause?


Quoting Peter Cock <p.j.a.c...@googlemail.com>:

On Tue, Sep 10, 2013 at 9:16 AM, Hans-philipp Brachvogel
<hans-philipp.brachvo...@student.uni-tuebingen.de> wrote:
Hey Dave,

thanks for the reply! Guess I wrote too much and explained badly what I
meant. I had already tested the Managed Tool Dependencies, but my problem
was that those only work for <requirement type="package">xyz</requirement>

They do not handle <requirement type="binary"... or <requirement
type="python-module", which is what I am looking for (beacuse of our special
setting). Anyhow, I searched a bit and found in
galaxy_dir/lib/galaxy/tools/__init__.py. at line 2671:

    if requirement.type in [ 'package', 'set_environment' ]:
        script_file, base_path, version =

So I changed that line to:

    if requirement.type in [ 'package', 'set_environment', 'binary',
'python-module' ]

This works, for me. If I have e.g.: <requirement
type="python-module">rpy</requirement> I can now use
dep_dir/rpy/default/env.sh to also load R into the environment.

Now, I wonder if that change will have any bad consequences? I could not
find anything about the requirement type 'binary' and 'python-module', what
are they normally needed for? Could this be relevant when using tool-shed?


These dependency declarations pre-date the Tool Shed and are
(as far as I know) ignored by the Tool Shed. They may currently
be non-functional, but I think they could be useful with a little
magic added to the Galaxy jobs to check the dependency as
part of the shell script submitted for the job (to give nice clear
failure errors about missing dependencies, rather than what
ever cryptic error the tool may give).


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:

To search Galaxy mailing lists use the unified search at:

Reply via email to