Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-24 Thread Carlos Borroto
On Mon, Sep 23, 2013 at 3:41 PM, John Chilton chil...@msi.umn.edu wrote: So you want this: action type=setup_virtualenvdocopt==0.6.1 python-levenshtein==0.10.2 biopython==1.62 ngs-tools==0.1.6 /action Newline between dependencies, and no whitespace to the left of each package. Hi John, I

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread Carlos Borroto
On Mon, Sep 23, 2013 at 1:57 PM, John Chilton chil...@msi.umn.edu wrote: On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Carlos! Hi, I have created a tool that depends on biopython. I don't like the idea of having several copies of

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread John Chilton
On Mon, Sep 23, 2013 at 1:09 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Sep 23, 2013 at 1:57 PM, John Chilton chil...@msi.umn.edu wrote: On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Carlos! Hi, I have created a tool

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread Carlos Borroto
On Mon, Sep 23, 2013 at 1:51 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: I'm installing my package using the virtualenv option. As you can see below I marked biopython as prior_installation_required=True. However, I can see that virtualenv is installing a copy of

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread John Chilton
On Mon, Sep 23, 2013 at 1:25 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Am Montag, den 23.09.2013, 12:57 -0500 schrieb John Chilton: On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Carlos! Hi, I have created a

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread Carlos Borroto
On Mon, Sep 23, 2013 at 2:22 PM, John Chilton chil...@msi.umn.edu wrote: Hi John, First let me tell you why I think duplicating the biopython install reduces reproducibility. I have this on my tool setup.py: install_requires=[ docopt, biopython,

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread John Chilton
On Mon, Sep 23, 2013 at 2:30 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Sep 23, 2013 at 2:22 PM, John Chilton chil...@msi.umn.edu wrote: Hi John, First let me tell you why I think duplicating the biopython install reduces reproducibility. I have this on my tool setup.py:

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread John Chilton
Opps, sent that last mail out before I meant to. On Mon, Sep 23, 2013 at 2:30 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Sep 23, 2013 at 2:22 PM, John Chilton chil...@msi.umn.edu wrote: Hi John, First let me tell you why I think duplicating the biopython install reduces

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread Carlos Borroto
On Mon, Sep 23, 2013 at 2:24 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Can you try to insert that (maybe adopt, its not checked): action type=set_environment_for_install repository name=package_biopython_1_62 owner=biopython package name=biopython version=1.62 /

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread Björn Grüning
Hi Carlos! Hi, I have created a tool that depends on biopython. I don't like the idea of having several copies of biopython around and also for best practice making workflows using my tool reproducible, I chose to make my package repository[1] dependent of package_biopython_1_62.

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread Björn Grüning
Am Montag, den 23.09.2013, 12:57 -0500 schrieb John Chilton: On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Carlos! Hi, I have created a tool that depends on biopython. I don't like the idea of having several copies of biopython

Re: [galaxy-dev] Repository tool dependencies and virtualenv install

2013-09-23 Thread John Chilton
On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Carlos! Hi, I have created a tool that depends on biopython. I don't like the idea of having several copies of biopython around and also for best practice making workflows using my tool