Hello Peter,
On Feb 20, 2014, at 10:20 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Your installation recipe for mira attempts to download a
On Thu, Mar 6, 2014 at 4:53 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 20, 2014, at 10:20 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
The BLAST+ packages have the same glitch in their fall-back
(so I will
On Thu, Mar 6, 2014 at 5:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Mar 6, 2014 at 4:53 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 20, 2014, at 10:20 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi Peter,
On Mar 6, 2014, at 1:07 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Mar 6, 2014 at 5:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Mar 6, 2014 at 4:53 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 20, 2014, at 10:20 AM, Greg Von Kuster g...@bx.psu.edu
Peter,
The test result at 13:11:20 is due to me manually running the install
and test framework to test the fabric replacement code I introduced. The
test result at 16:16:58 is due to the repository preparation script
running successfully at its scheduled time, initializing the tool test
Peter,
Correction: I mistakenly thought your email was regarding a repository
on the main tool shed, against which I manually ran the test framework.
Now that I noticed that you're referring to a repository on the test
tool shed, the 13:10 test result is because the test tool shed's test
,
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster g...@bx.psu.edu wrote:
In any case, we have a fix for out move_directory_files which
Dave is now committing. So your tests should pass with tonight's
run -
if a tool failed we all really benefit from seeing as much as we can - as
securely as we can.
Can we safely expose them somewhere protected?
On Thu, Feb 20, 2014 at 8:59 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
,
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Your installation recipe for mira attempts to download a binary and if that
fails, it echoes an error, but still performs set_environment
Hi Peter,
Regarding youyr previous question about why the more usefule log resutls are
not returned for display in the Tool Shed, the reason is that our use of
fabric's local command for installing tool dependnecies restricts us from
bewing able to capture that information. We are currently
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
We'll try to get some time to look at your tool_dependencies.xml recipe as
soon as possible.
Greg Von Kuster
Hi Greg,
Overnight this has gone back to the previously observed missing
data problem (e.g.
Hello Peter,
Please see below…
On Feb 19, 2014, at 4:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg,
Overnight this has gone back to the previously observed missing
data problem (e.g. email of 4th Feb) - no test results at all:
On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
Please see below...
...
Your above email arrived in my inbox at 4:42 AM EST, and
it looks like your repository in question was not yet tested.
Ah. That would partly explain things - perhaps coupled with
Hi Peter,
Dave B and I just discovered that issue that causes your tests to fail.
The problem lies with our current implementation supporting the
move_directory_files action tag, which is used in your recipe. This tag
ultimately uses Python's os.listdir via shutil.move.
It turns out that
On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Dave B and I just discovered that issue that causes your tests to fail.
The problem lies with our current implementation supporting the
move_directory_files action tag, which is used in your recipe.
This tag
Hi Peter,
On Feb 19, 2014, at 6:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Dave B and I just discovered that issue that causes your tests to fail.
The problem lies with our current implementation
On Mon, Feb 17, 2014 at 3:08 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
It looks like you made some changes to your tool dependency
recipe since the last test run.
Yeah, the mira de novo test was missing
Hi Peter,
We'll try to get some time to look at your tool_dependencies.xml recipe as soon
as possible.
Greg Von Kuster
On Feb 18, 2014, at 5:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg, Dave,
RE: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Same as
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
We'll try to get some time to look at your tool_dependencies.xml recipe as
soon as possible.
Greg Von Kuster
Great.
Re:
https://trello.com/c/HVGrShnC/60-tool-shed-should-test-installation-of-packages
On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Returning to the MIRA4 problem, I got a meaningful test
failure which
Hi Peter,
It looks like you made some changes to your tool dependency recipe since the
last test run. Dave B and I followed the latest revision of your recipe and
manually installed it using
On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
It looks like you made some changes to your tool dependency
recipe since the last test run.
Yeah, the mira de novo test was missing the test-data input files.
But I didn't touch mirabait or the install XML
Hi Peter,
On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Moreover there is a similar problem with the matching repository
on the Test Tool Shed,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-04 showing failed tests for
On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Moreover there is a similar problem with the matching repository
on the Test Tool Shed,
Hi Peter,
The following issue was corrected in change set
https://bitbucket.org/galaxy/galaxy-central/commits/e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211
On Jan 29, 2014, at 12:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Peter,
I've created the following Trello card for this. I know what the problems are,
but I won't have time to get fixes for them for a while. Please continue to
reposrt issues you discover and I'll make sure to get fixes as soon as I get
time.
Hi Peter,
I've created the following Trello card for this. I know what the problems are,
but I won't have time to get fixes for them for a while. Please continue to
reposrt issues you discover and I'll make sure to get fixes as soon as I get
time.
On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Peter wrote:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-29 missing blast_datatypes dependency (why?)
2014-01-28 showing
Hi Peter,
On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-29 missing blast_datatypes dependency (why?)
2014-01-28 showing failed tests for sambamba_filter (wrong tool)
I'll have
On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-29 missing blast_datatypes dependency (why?)
Hi all,
Are both the main and test Tool Sheds currently meant to be running
nightly tests again?
I've not really got back into Galaxy tool testing since Christmas.
Most of my tools'
test results look sensible, but there seem to be some issues still, e.g.
Hi Peter,
On Jan 29, 2014, at 12:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
Are both the main and test Tool Sheds currently meant to be running
nightly tests again?
Yes
I've not really got back into Galaxy tool testing since Christmas.
Most of my tools'
test results
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