Re: [galaxy-dev] Adding a Tool for PANAMA

Thanks Ross and Peter. That worked. I think I will keep the Python wrapper though, gives me more control :) Saket On 3 June 2013 16:48, Ross wrote: > Hi Saket > If you want to redirect the executable's stdout to a new Galaxy dataset > you've defined as $output, something like: > > '$output' >

Re: [galaxy-dev] Adding a Tool for PANAMA

Hi Saket, I haven't looked at this but I noticed the following advice on their web site: If you want to call PANAMA directly from python, just take a look at the PANAMA function inpanama.core.run. Do you have a plan for representing the required incoming expression and snp matrices in Galaxy? AFA

Re: [galaxy-dev] Problems running functional tests

Ira, Yes, I should have mentioned that due to the way functional tests are executed, an environment variable needs to be explicitly exported before the functional test framework will recognize it. The syntax is very nearly the same: export GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_depen

Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

Hello Jens. What is the name of the repository you are trying to install from the tool shed? Can you run the following sql in your database and reply back with the results? select id, name, owner, installed_changeset_revision, changeset_revision, deleted, status, error_message from tool_shed_

Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

Hi Jens, Thanks for the information, but it doesn't help determine what is causing this behavior in your environment. It's strange that you have never installed the ncbi_blast_plus repository (so it is not currently in some error state), and yet you cannot install it. I am not able to reprodu

Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

Hi Greg, Thanks a lot for your email. I hope, I did do not misunderstand something. We are trying to install "ncbi_blast_plus" from the "Galaxy main tool shed". As we did not manage to install "ncbi_blast_plus" the "where" clause does not make sense to me. Hence, I omit it. Here is the result.

[galaxy-dev] GCC2013 Regular Registration closes June 14

Hello all, This is a reminder that registrationfor the 2013 Galaxy Community Conference (GCC2013) closes June 14*, just ten days from today. *Registering now

Re: [galaxy-dev] Problems running functional tests

Oops ... I should have thought of that Thanks .. it works now. Ira On 04/06/2013, at 11:20 PM, Dave Bouvier wrote: > Ira, > > Yes, I should have mentioned that due to the way functional tests are > executed, an environment variable needs to be explicitly exported before the > functional te

Re: [galaxy-dev] mapping Summary from Bowtie

> > how to get the mapping summary from bowtie2 using galaxy interface.. This isn't possible right now, but I've filed a Trello card that you can follow to watch progress on this enhancement: https://trello.com/c/yFeXvhUg Of course, a patch/contribution addressing this issue would be fantastic

Re: [galaxy-dev] Adding a Tool for PANAMA

Hi Ross, On 4 June 2013 16:15, Ross wrote: > Hi Saket, > I haven't looked at this but I noticed the following advice on their web > site: > > If you want to call PANAMA directly from python, just take a look at the > PANAMA function inpanama.core.run. > > Do you have a plan for representing t