In general, see if the new package is available in conda-forge or
bioconda. If so, you just need to mention it in the requirements
section of the tool XML.
Devon Ryan, Ph.D.
Max Planck Institute of Immunobiology and Epigenetics
On Mon, Jul 24, 2017 at 12:21 PM, Delisle Lucille
> Hello Devon,
> Thank you very much for your quick answer. In fact in my
> tool_dependencies.xml I did not put the '#':
> The log has been sent in a different e-mail (sorry).
> I think the conda is a really good alternative but I did not know how to ask
> conda to resolve it.
> In fact, I need numexpr to install another python library and I do not know
> how to write in this new package how to look for numexpr with conda.
> Thanks again,
> Lucille Delisle, PhD
> PostDoc Duboule Lab
> Laboratory of Developmental Genomics
> EPFL SV ISREC UPDUB
> SV 2843
> Station 19
> CH-1015 Lausanne
> Tel : +41 21 693 97 08
> De : dprya...@gmail.com <dprya...@gmail.com> de la part de Devon Ryan
> Envoyé : lundi 24 juillet 2017 12:06
> À : Delisle Lucille
> Cc : firstname.lastname@example.org
> Objet : Re: [galaxy-dev] Creating a tool dependency packages
> You can remove everything starting with the "#" in the URL, though I
> presume that's not the problem. Have a look in the installation log on
> your machine, perhaps there's an error message somewhere in it.
> More conveniently, though, numexpr-2.6.2 is available in conda-forge,
> so if you use conda as a dependency resolver then you can skip
> creating a tool dependency package. This saves a LOT of hassle, in my
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> On Mon, Jul 24, 2017 at 11:58 AM, Delisle Lucille
> <lucille.deli...@epfl.ch> wrote:
>> Dear Galaxy list,
>> I do not know if it is the right place to ask my question. I would like to
>> create a tool dependency package for numexpr (a python library).
>> I tried to do it taking examples from different tool dependency packages
>> from iuc for example.
>> I added my repository to the testtoolshed but when I tried to install it.
>> The directory lib/python of my tool is empty.
>> My repository is : package_python_2_7_numexpr_2_6_2
>> The big difference I see between the one from iuc and mine is the url:
>> For example, for pybigwig, the URL is :
>> For my library numexpr I could not find such a url so I put the one I
>> thought would be the good one:
>> Thank you very much for your help,
>> Lucille Delisle, PhD
>> PostDoc Duboule Lab
>> Laboratory of Developmental Genomics
>> EPFL SV ISREC UPDUB
>> SV 2843
>> Station 19
>> CH-1015 Lausanne
>> Tel : +41 21 693 97 08
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