Hi, I wonder if there's some kind of documentation (reference) for the Galaxy source? At the moment I have a couple of questions for example. 1. How can I get the dataset object (in my Python wrapper) given the dataset name? 2. How can I access the job parameters (enered in the UI or 'hidden') in the Python code? In general, when I have this kind of questions, where do I look? -Alex
The API allows you to do some of that... If you pass it the ID of the object (input.id) you can do all kinds of requests with the API. Look in the scripts/api folder of your local Galaxy instance... NOTE: The API seems to be a bit of a stepchild, since there is no good documentation and it seems to be undeveloped to some extent. For instance, the biggest issues is that you cannot pass a workflow any parameters, only inputs and outputs... So caveat emptor! Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer@me.com LinkedIn Profile On Oct 22, 2012, at 5:26 PM, Alex.Khassapov@csiro.au wrote:
Hi, I wonder if there’s some kind of documentation (reference) for the Galaxy source?
At the moment I have a couple of questions for example.
1. How can I get the dataset object (in my Python wrapper) given the dataset name? 2. How can I access the job parameters (enered in the UI or ‘hidden’) in the Python code?
In general, when I have this kind of questions, where do I look?
-Alex ___________________________________________________________ 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:
API seems a bit of overkill, as I understand, it's useful for 'external' access via http. My tools run inside Galaxy and I should be able to use Python code directly. From: Anthonius deBoer [mailto:thondeboer@me.com] Sent: Tuesday, 23 October 2012 12:16 PM To: Khassapov, Alex (CSIRO IM&T, Clayton) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Source code documentation The API allows you to do some of that... If you pass it the ID of the object (input.id) you can do all kinds of requests with the API. Look in the scripts/api folder of your local Galaxy instance... NOTE: The API seems to be a bit of a stepchild, since there is no good documentation and it seems to be undeveloped to some extent. For instance, the biggest issues is that you cannot pass a workflow any parameters, only inputs and outputs... So caveat emptor! Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer@me.com<mailto:thondeboer@me.com> LinkedIn Profile<http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b> On Oct 22, 2012, at 5:26 PM, Alex.Khassapov@csiro.au<mailto:Alex.Khassapov@csiro.au> wrote: Hi, I wonder if there's some kind of documentation (reference) for the Galaxy source? At the moment I have a couple of questions for example. 1. How can I get the dataset object (in my Python wrapper) given the dataset name? 2. How can I access the job parameters (enered in the UI or 'hidden') in the Python code? In general, when I have this kind of questions, where do I look? -Alex ___________________________________________________________ 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: http://lists.bx.psu.edu/
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Alex.Khassapov＠csiro.au -
Anthonius deBoer