[galaxy-dev] (Composite) Dataset Upload not Setting Metadata

2011-09-12 Thread Paniagua, Eric
Hi everyone, I've been getting my feet wet with Galaxy development working to get some of the rexpression tools online, and I've run into a snag that I've traced back to a set_meta datatype method not being able to find a file from which it wants to extract metadata. After reading the code, I

Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata

2011-09-13 Thread Paniagua, Eric
...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric [epani...@cshl.edu] Sent: Monday, September 12, 2011 7:37 PM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata Hello again, It looks like

Re: [galaxy-dev] uploading binary files checksum changes, Galaxy doing something to file?

2011-09-16 Thread Paniagua, Eric
Hi Leandro, Is there an entry in your history for the upload? What file format does it show? Is there any chance your original file was zipped? If Galaxy detected it as a zip file on upload, it may have unzipped it and taken the first file in it as the dataset. That's at least the version

[galaxy-dev] 2 questions about Galaxy's functional testing support

2011-09-29 Thread Paniagua, Eric
Hi all, I've read the Wiki page on Writing Functional Tests (http://wiki.g2.bx.psu.edu/Admin/Tools/Writing%20Tests) and I've been looking through test/base and test/functional and I am left with two questions: * Is it possible to write a test to validate metadata directly on an

Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata

2011-10-03 Thread Paniagua, Eric
...@bx.psu.edu] Sent: Monday, October 03, 2011 2:00 PM To: Paniagua, Eric Cc: Nate Coraor; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata Hi Eric, Can you provide an example of the composite datatype that is experiencing the metadata problems

Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata

2011-10-03 Thread Paniagua, Eric
/filters/cutWrapper.xml) can be used to set metadata ( e.g. column assignments ) on tool outputs without using hooks. Please let us know if we can provide additional information. Thanks for using Galaxy, Dan On Sep 30, 2011, at 1:15 PM, Paniagua, Eric wrote: Hi Nate, Thanks for your answers. I

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

2011-11-30 Thread Paniagua, Eric
and specifically on the radar of the primary developer(s) / maintainer(s) of the testing framework? Thanks again for responding to my email. Best, Eric From: Greg Von Kuster [g...@bx.psu.edu] Sent: Wednesday, November 30, 2011 9:56 AM To: Paniagua, Eric Cc: galaxy

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

2011-11-30 Thread Paniagua, Eric
day :) Best, Eric From: Greg Von Kuster [g...@bx.psu.edu] Sent: Wednesday, November 30, 2011 1:22 PM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Dev Subject: Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional

Re: [galaxy-dev] [Internal - Galaxy-dev #2159] (New) 2 questions about Galaxy's functional testing support

2011-12-06 Thread Paniagua, Eric
for expressly letting me know; that is much appreciated. Happy hacking, Eric From: Nate Coraor [n...@bx.psu.edu] Sent: Tuesday, December 06, 2011 1:04 PM To: Greg Von Kuster Cc: Paniagua, Eric; galaxy-dev@lists.bx.psu.edu Dev Subject: Re: [galaxy-dev] [Internal

Re: [galaxy-dev] Managing Data Locality

2013-11-08 Thread Paniagua, Eric
From: jmchil...@gmail.com [jmchil...@gmail.com] on behalf of John Chilton [chil...@msi.umn.edu] Sent: Tuesday, November 05, 2013 11:58 AM To: Paniagua, Eric Cc: Galaxy Dev [galaxy-...@bx.psu.edu] Subject: Re: [galaxy-dev] Managing Data Locality Hey Eric, I think what you are purposing would

Re: [galaxy-dev] Managing Data Locality

2013-11-08 Thread Paniagua, Eric
for your time and assistance. Best, Eric From: jmchil...@gmail.com [jmchil...@gmail.com] on behalf of John Chilton [chil...@msi.umn.edu] Sent: Tuesday, November 05, 2013 11:58 AM To: Paniagua, Eric Cc: Galaxy Dev [galaxy-...@bx.psu.edu] Subject: Re: [galaxy-dev

[galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

2014-05-23 Thread Paniagua, Eric
Dear Galaxy Developers, I've been banging my head against this one for a few days now. I have two Galaxy instances. One resides on a server called genomics, which also hosts the corresponding PostgreSQL installation. The second also resides on genomics, but its database is hosted on

Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

2014-05-27 Thread Paniagua, Eric
is now completely empty. Have you ever seen this before? Thanks, Eric From: Dannon Baker [dannon.ba...@gmail.com] Sent: Tuesday, May 27, 2014 7:40 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL

Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

2014-05-27 Thread Paniagua, Eric
in... From: Dannon Baker [dannon.ba...@gmail.com] Sent: Tuesday, May 27, 2014 11:43 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host On Tue, May 27, 2014 at 11:26 AM, Paniagua

Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

2014-05-27 Thread Paniagua, Eric
that things are working as expected. However, just the fact that this job is running is a very good sign. From: Dannon Baker [dannon.ba...@gmail.com] Sent: Tuesday, May 27, 2014 11:58 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev

Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host

2014-05-27 Thread Paniagua, Eric
Restarting the Galaxy server in multiple process mode appears to have helped. The test job is now running. From: Paniagua, Eric Sent: Tuesday, May 27, 2014 12:43 PM To: Dannon Baker Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Problem using Galaxy