Yes :(
There's been some past discussion of this from a tool developer
perspective, e.g. https://trello.com/c/JnhOEqow and
http://dev.list.galaxyproject.org/Using-input-dataset-names-in-output-dataset-names-td4662481.html
The best individual tool authors can do is something like
"$input.name proc
Hi Michael,
I was just looking for the khmer Galaxy wrappers in order to try
diginorm on some high coverage data, but they are not yet in
the main ToolShed are they? I found this on the Test Tool Shed:
https://testtoolshed.g2.bx.psu.edu/view/crusoe/khmer
The last update date seems to match the c
Good sleuthing Evan :)
That explains this strange error I was getting:
http://dev.list.galaxyproject.org/MarkupSafe-egg-missing-e-args-1-key-e-args-0-key-tc4666021.html
(In that case I switched to using a virtualenv)
Peter
On Wed, Nov 26, 2014 at 6:11 PM, Evan Bollig PhD wrote:
> I tested all
.
Regards,
Peter
On Wed, Nov 19, 2014 at 5:57 PM, Peter Cock wrote:
> Thanks John,
>
> Fingers crossed we'll get some more detailed logs in a day or two :)
>
> Peter
>
> On Wed, Nov 19, 2014 at 5:48 PM, John Chilton wrote:
>> Hey Peter,
>>
>> Dave is ou
Hi Simon,
I was looking for a Trimmomatic wrapper for Galaxy (which I have thus
far only used at the command line outside of Galaxy), and while there
does not seem to be one in the main Tool Shed, I see you have been
working on this over on the Test Tool Shed:
https://testtoolshed.g2.bx.psu.edu/v
file.
Regards
PeterC
On Fri, Nov 28, 2014 at 2:31 PM, Peter Cock wrote:
> Hi Simon,
>
> I was looking for a Trimmomatic wrapper for Galaxy (which I have thus
> far only used at the command line outside of Galaxy), and while there
> does not seem to be one in the main Tool Shed,
Galaxy workflows are stored in the database, but can be exported
in JSON format (intended for importing into another Galaxy server).
Peter
On Wed, Dec 3, 2014 at 3:38 PM, Weiyan Shen wrote:
> Hi ,
> As we know galaxy tools work with the python,perl,and other tools script in
> galaxy-dist/tools,b
Hi Wolfgang,
You didn't include the name or a link to your Test Tool Shed packages.
Are you talking about the suite_config.xml file?
I'm not sure if Galaxy still uses that, no-one answered my earlier question:
http://dev.list.galaxyproject.org/Role-of-suite-config-xml-in-current-Tool-Shed-tc46658
Hi all,
The "Repository dependency definitions" link is working on the
Main Tool Shed, but fails with the following exception on the
Test Tool Shed:
URL: http://testtoolshed.g2.bx.psu.edu/repository/browse_repository_dependencies
File
'/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/web/f
On Thu, Nov 27, 2014 at 1:58 PM, Peter Cock wrote:
> Hi Guys,
>
> I retitled this since the TestToolShed does seem to be running tests
> regularly again. However, I still have a fair number failing with the
> cryptic status "Exception: History in error state."
>
> I
wner="wolma"
> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
> owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu"; />
> name="mimodd_annotate_variants" owner="wolma"
> toolshed="https://t
On Wed, Dec 10, 2014 at 2:03 PM, John Chilton wrote:
> On Wed, Dec 10, 2014 at 5:46 AM, Peter Cock wrote:
>> Hi guys,
>>
>> The good news is my list of failing tools has shrunk to the following,
>> none of which seem to have been tested yet in December, stuck
>&
On Wed, Dec 10, 2014 at 2:08 PM, John Chilton wrote:
> Peter -
>
> When you have previously asked about suite_config.xml I grepped
> around and I couldn't find any references to it, did some more greps
> just now and I still cannot. My best guess is that is not being used
> at all - but I am not
Hi Peter B,
Originally the tests were nightly, but due to the rising load
this was dropped to every two or three days. As far as I
know that is still the goal.
Unfortunately the tool shed test system seems to be somewhat
broken at the moment, see this thread starting last month:
http://dev.list.
On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu wrote:
> Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join
> didn't work. What did I do wrong?
> I installed join from galaxy main tool shed, bx_python_0_7 was installed but
> with installation Status "missing tool dependencies".
>
>.
Hi all,
Using gzipped input files in tool functional tests (which would be
decompressed by the upload tool) used to work, e.g.
https://travis-ci.org/peterjc/pico_galaxy/builds/42395911
https://github.com/peterjc/pico_galaxy/blob/539260fa4348ed454ce464e48c9dbbccca22a012/tools/seq_filter_by_mapping
axy/galaxy-central/commits/a74d32014b0512613042c2a44d0b946703a1fbcd
>
> The commit also includes a test case so hopefully this won't break again.
>
> -John
>
> On Wed, Dec 17, 2014 at 6:56 AM, Peter Cock wrote:
>> Hi all,
>>
>> Using gzipped input files in tool functiona
Do you have a matching dependency
declaration in mytool.xml?
Peter
On Mon, Dec 22, 2014 at 9:56 AM, KRESS Arnaud (ESP) wrote:
> Hi gentlemen,
> I am currently struggling to create a custom package (to share via a
> toolshed) that would include a tool definition file and the associated
> binary
Unfortunately the ToolShed dependency only provides samtools to individual
Galaxy tools that declare a dependency on it. However, it allows multiple
versions of samtools to be available to different (versions of) Galaxy
tools.
This does NOT provide a samtools on $PATH for Galaxy itself, and it nee
Yes ;)
Are you writing your own tool, or trying to install someone else's?
There are two basic options,
(1) Install Biopython into the default Python used when jobs are
run. Simple, but manual - and you can only have one version.
This is actually what we are still doing on our local Galaxy
since
On Tue, Jan 6, 2015 at 12:23 AM, Peter Cock wrote:
> Yes ;)
>
> Are you writing your own tool, or trying to install someone else's?
>
> There are two basic options,
>
> (1) Install Biopython into the default Python used when jobs are
> run. Simple, but manual - and
any new
> errors crop up.
>
>--Dave B.
>
>
> On 12/10/2014 09:19 AM, Peter Cock wrote:
>>
>> On Wed, Dec 10, 2014 at 2:03 PM, John Chilton wrote:
>>>
>>> On Wed, Dec 10, 2014 at 5:46 AM, Peter Cock
>>> wrote:
>>>>
>>
On Thu, Jan 8, 2015 at 3:27 AM, Jeltje van Baren
wrote:
> Hi,
>
> I'm trying to find out what the best way is to see if my functional tests
> work as expected, and I'm also wondering when these tests are (supposed to
> be) run. Here are the details:
>
> Following instructions at
> https://wiki.gal
On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque
wrote:
> Hello Galaxy,
>
> I'm currently working on adding some tools and am having an issue with
> DELLY.
>
> So, I am under the impression that BAM indexing happens automatically when a
> BAM is uploaded. However there is no associated dataset_i.
Hi Ryan,
The problem isn't Galaxy stripping the extension, rather
Galaxy is actually decompressing the file as part of the
upload process.
Unfortunately (and there is an open Trello enhancement
request on this), Galaxy does not support sorting any of
the defined datatypes in compressed form UNLES
n Mon, Jan 12, 2015 at 4:52 PM, Ryan G wrote:
> Galaxy is not decompressing the file. The file is linked to on the
> filesystem.
>
> On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock
> wrote:
>>
>> Hi Ryan,
>>
>> The problem isn't Galaxy stripping the extensio
as unaware of how to access metadata, that seemed to be my issue. The
> tool works now though!
>
> Thanks so much,
>
> Marco
>
>
>
>
> On 2015-01-09 7:13 PM, "Peter Cock" > wrote:
> >
> >I think the symlink approach is best, see for example th
, Jan 12, 2015 at 12:14 PM, Peter Cock
> wrote:
>>
>> Ah. Then this is more subtle... are you using the
>> library import option where Galaxy just symlinks
>> to existing files? I thought that was not possible
>> with gzipped files (for the reasons given below).
&g
On Thu, Jan 15, 2015 at 6:57 PM, Ryan G wrote:
> Because of the way the infrastructure for my Galaxy instance is set up, I
> need to download and install tools from the toolshed manually. For most of
> the tools, this is pretty easy, however I'm now trying to add RSEM to my
> instance and it has
I think this is the (relatively new) Galaxy ability to automatically
run N copies of your tool given N input files, making N outputs
and is related to the collections work.
(This is possible if your tool takes a single input file)
Peter
On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan
wro
On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier wrote:
> Peter,
>
> After fixing a number of issues, it appears that the tests are now running
> as they should. I'll keep an eye on the test framework in case any new
> errors crop up.
>
>--Dave B.
Thanks Dave,
Yes, the good news is tests are now
On Tue, Jan 27, 2015 at 11:32 AM, Peter Cock wrote:
> On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier wrote:
>> Peter,
>>
>> After fixing a number of issues, it appears that the tests are now running
>> as they should. I'll keep an eye on the test framework i
Hi all,
I have a query about a failing tool test on the Tool Shed, where it
seems Galaxy is trying to convert both the expected BAM output
and the tool's BAM output into SAM for comparison - but this
fails.
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-27 02:13:51
...
Tool i
On Tue, Jan 27, 2015 at 1:25 PM, Peter Cock wrote:
>
> On Tue, Jan 27, 2015 at 11:32 AM, Peter Cock
> wrote:
> > On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier wrote:
> >> Peter,
> >>
> >> After fixing a number of issues, it appears that the tests are
On Thu, Jan 29, 2015 at 12:08 PM, Peter Cock wrote:
> On Tue, Jan 27, 2015 at 1:25 PM, Peter Cock wrote:
>>
>> On Tue, Jan 27, 2015 at 11:32 AM, Peter Cock
>> wrote:
>> > On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier wrote:
>> >> Peter,
>> >
On Fri, Jan 30, 2015 at 2:07 PM, Dannon Baker wrote:
> On Fri Jan 30 2015 at 5:36:29 AM Peter Cock
>>
>> >> https://toolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owner=peterjc&status=all
>> >>
>> >> Internal Server Error
>>
Retitling thread,
On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock wrote:
> Thanks Dave,
>
> The good news is yes, the tests are running again on the
> Test Tool Shed (although not the main Tool Shed yet), and
> many of my tools now have successful test results from
> last nigh
ion testing, but those seem to be fixed with
>> latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d .
>>
>> Nicola
>>
>> Il 30.01.2015 17:36 Peter Cock ha scritto:
>>
>> Retitling thread,
>>
>> On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock
>> wrote:
&
Hi Philippe,
All the Galaxy tool definitions ought to have a
tag which is run immediately before the actual string
(on the same cluster etc). That captures version text from the
actual binary used for generating a history entry, and is recorded
in the job's meta data.
Currently this is not cros
On Fri, Jan 30, 2015 at 5:24 PM, Peter Cock wrote:
> Hi Dannon, Nicola,
>
> This sounds very promising - I'll rerun the TravisCI job and we can
> expect it to work this time :)
>
> https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251
Hi Roberto, Hans-Rudolf,
I can confirm from personal testing that enabling the
parallelism task-splitting in Galaxy does not work
well with SQLite.
This caused me problems with development and
testing since my development Galaxy instance uses
SQLite. As you found, testing with smaller splits
is o
On Fri, Feb 6, 2015 at 9:59 AM, Roberto Alonso CIPF wrote:
> Hello,
>
> Postgres did it perfectly, but as I would like to enable this option in my
> production servers I changed two configs in galaxy.ini:
>
> # This enables splitting of jobs into tasks, if specified by the particular
> tool config
On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion wrote:
> I was trying to track down why an attempt to test my tool is eventually
> failing with:
>
> "ValueError: No such test TestForTool_ffp_phylogeny"
>
There are at least two reasons that can happen.
(a) The tool wasn't loaded by the test fram
Hi Roberto,
It looks like this is a known issue with FASTQ splitting,
https://trello.com/c/qRHLFSzd/1522-issues-with-tasked-jobs-parallelism
I originally broke it during a refactor, but it looks like the
discussion died about that that method was meant to do
(e.g. FQTOC = FASTQ table of contents?
On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon wrote:
> I have a new galaxy installation on my server. I uploaded two fastq files
> and now I'm trying to run trimmomatic and fastqc. In both cases I am
> presented with a drop down list of fastq files to select from but the lists
> are empty. I
On Fri, Feb 13, 2015 at 11:38 AM, Nicola Soranzo wrote:
> Il 13.02.2015 03:17 Peter Cock ha scritto:
>>
>> Hi Roberto,
>>
>> It looks like this is a known issue with FASTQ splitting,
>>
>> https://trello.com/c/qRHLFSzd/1522-issues-with-tasked-jobs-paralleli
Thanks for the timely reminder Dave,
Note that the John Hopkins system seems to use Adobe Connect
which requires Flash Player 10.3 or above.
I don't have that on my laptop, but my main excuse for not joining
you all is I hadn't checked the start time based on my current
location, and unfortunatel
On Fri, Feb 20, 2015 at 3:56 PM, Lapointe, David
wrote:
> I tried installing biopython and dependancies from the toolshed but this
> does not seem to be functional even though these tools say INSTALLED.
How are you testing it? Any Galaxy copy of Biopython will not be
available to the system Pytho
On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon wrote:
>
> I figured that galaxy must be finding a samtools v1.1 even though the tool
> was not installed, according to the admin page. I uninstalled the samtools
> that was installed system-wide on the server. Now I get this error:
>
> Traceback (mos
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:
> The main problem for me was that I was not aware that the tophat
> tool had a dependency on a command line tool outside of galaxy
> installation. I see in the admin interface that tophat has a dependency
> on samtools of type package and I as
On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning
wrote:
> Am 24.02.2015 um 10:03 schrieb Peter Cock:
>> ... So far so good, but at that point Galaxy
>> tries to index the BAM file itself. This happens for any BAM file,
>> regardless of the tool which created it - and simply e
Hi all,
I'm trying the (BETA 2) GitHub repository with a view to switching
from hg for my Galaxy development. There are a couple of big
scary tracebacks in the stdout which look like SQLalchemy
incompatibilities - are these a recent issue?
$ git clone
$ cd galaxy
$ cp config/galaxy.ini.sample con
On Tue, Feb 24, 2015 at 2:57 PM, Dannon Baker wrote:
> Hi Peter,
>
> Yes, this is a known recent issue that I'm actually at work fixing right
> now.
>
> -Dannon
Great - I'll ignore this for now (it appears harmless for what
I want to do today).
Thanks,
Peter
On Tue, Feb 24, 2015 at 4:43 PM, Roberto Alonso CIPF wrote:
> Hello again,
>
> first of all thanks for your help, it is being very useful.
>
> What I have done up to now is to copy this method to the class Sequence
>
> def get_split_commands_sequential(is_compressed, input_name, output_name,
> sta
Hi all,
TL:DR abstract: Forgetting the "filter-with = proxy-prefix" gives
very confusing results. Hopefully this email will help someone
else who made the same configuration mistake.
--
As part of trying out the new (still in beta) Galaxy via git on GitHub
(rather than via hg on BitBucket), I am
On Wed, Feb 25, 2015 at 12:26 PM, Peter Cock wrote:
> Hi all,
>
> TL:DR abstract: Forgetting the "filter-with = proxy-prefix" gives
> very confusing results. Hopefully this email will help someone
> else who made the same configuration mistake.
>
And as a follow
On Wed, Feb 25, 2015 at 2:07 PM, Roberto Alonso CIPF wrote:
> Hello again :),
>
> I have found the problem, the code that merge the files is this:
> galaxy/datatypes/tabular.py:484:cmd = 'egrep -v "^@" %s >> %s' %
> ( ' '.join(split_files[1:]), output_file )
> This concatenates the fil
On Wed, Feb 25, 2015 at 3:34 PM, Roberto Alonso CIPF wrote:
> Perfect, Galaxy will also need to add the function that was deleted by
> merge, in galaxy/datatypes/sequence.py
Yes - if you want to do a pull request with that, please go ahead.
Otherwise I hope to do it later this week...
Your egrep
Hi all,
Using either the legacy upload tool, or the new upload widget, the
following FTP URL *appears* to load into Galaxy correctly giving
a green history entry.
However, on closer inspection it is an empty file with this peep text:
Unable to fetch
ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphel
On Wed, Feb 25, 2015 at 5:33 PM, Peter Cock wrote:
> Hi all,
>
> Using either the legacy upload tool, or the new upload widget, the
> following FTP URL *appears* to load into Galaxy correctly giving
> a green history entry.
>
> However, on closer inspection it is an empty fil
On Thu, Feb 26, 2015 at 10:59 AM, Pierre Lindenbaum
wrote:
> Hi Galaxy,
>
> I'm trying to put one of my java tool in galaxy.
>
> I've copied the required files in my tool directory under /tools/jvarkit (I
> can see it galaxy)
>
> $ ls
> commons-jexl-2.1.1.jar
> commons-logging-1.1.1.ja
On Thu, Feb 26, 2015 at 12:38 PM, Pierre Lindenbaum
wrote:
> Hi Peter,
>
>
> i wrote the tool_dependencies.xml
>
>
>
>
>
>
>
>
> action="set_to">$INSTALL_DIR
>
>
>
On Thu, Feb 26, 2015 at 1:35 PM, Pierre Lindenbaum
wrote:
>> You'll need to white list the semi-colon which Galaxy has replaced as a
>> security precaution (user free text can be exploited). See here:
>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter
>
>
> Thanks: adding :
>
>
On Thu, Feb 26, 2015 at 2:43 PM, John Chilton wrote:
>
> Also not need to escape $__tool_directory__ (so use
> $__tool_directory__ instead of \$__tool_directory__).
>
> -John
If this was unclear, $VAR in the XML fragment
is taken to be a Python variable available within the Cheetah
parser. Typi
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton wrote:
> Yeah - that is unfortunate - I agree completely that the resulting
> datasets should be red. I have created a Trello card here:
>
> https://trello.com/c/A6LrdjUU
>
> -John
Thanks John,
Does the new "Download from URL or upload files from dis
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton wrote:
> Yeah - that is unfortunate - I agree completely that the resulting
> datasets should be red. I have created a Trello card here:
>
> https://trello.com/c/A6LrdjUU
>
> -John
I just commented on the Trello issue - as John implied with
the issue
On Thu, Feb 26, 2015 at 11:53 PM, Dooley, Damion wrote:
> Helop aI've been testing (using planemo) some tools scheduled for toolshed
> publication. My first test works, but Galaxy reports that the second one
> fails with:
>
> "Parameter %s requires a value, but has no legal values defined" % se
Hi all,
I've been using the SQLite template database feature to speed up
functional testing. Rather than starting for the initial schema and
applying all the incremental changes (as done when installing a
fresh Galaxy instance), this lets the test suite start with a recent
version of the database,
On Fri, Feb 27, 2015 at 2:15 PM, John Chilton wrote:
> Hey Peter,
>
> That database is pretty new (not yet in stable) - but you are
> tracking the master branch of galaxy on github in your tests (which is
> sortof like stable). You will want to either track the dev branch (so
> you can continue
On Fri, Feb 27, 2015 at 8:58 PM, Dooley, Damion wrote:
> First, hey Peter, thanks for input! I'd seen the explicit piping before,
> couldn't remember its format though; I will switch to it.
>
> Well, after a morning of testing, I see the test system is actually
> finding the repeat section variab
On Fri, Feb 27, 2015 at 10:36 PM, Dooley, Damion wrote:
> Yay, with your tip, galaxy direct tests now work with tool_conf.xml AND data
> table in place!
>
> Galaxy DOC person: please update
> https://wiki.galaxyproject.org/Admin/RunningTests
> to state that tool_conf.xml.sample is NOT used for t
On Mon, Mar 2, 2015 at 4:08 PM, Roberto Alonso CIPF wrote:
> Hello,
>
> I would like to add a very simple GATK wrapper to galaxy, but I am facing
> one problem. When you want to use UnifiedGenotyper tool, the extension of
> the bam file must be .bam, and when you upload something to galaxy it
> ch
Hi Damion,
I see your blast_reporting tool is now on the Main Tool Shed.
https://toolshed.g2.bx.psu.edu/view/damion/blast_reporting
I am a little confused about your tabular output options:
Standard 12 columns
Standard 12 columns + sequences
Extended 24 columns
Extended 26 columns
Only field sel
Hello all,
Good news - automated testing on the Galaxy Tool Shed
seems to be mostly working again (after a period of trouble
in the New Year). Thanks Dave B. et al, I'm sure this has
been a lot of effort behind the scenes. I'm looking forward
to getting a clean sweep of passing tests again...
I c
On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock wrote:
> Hi all,
>
> I have a query about a failing tool test on the Tool Shed, where it
> seems Galaxy is trying to convert both the expected BAM output
> and the tool's BAM output into SAM for comparison - but this
> fails.
On Tue, Mar 3, 2015 at 9:51 AM, Peter Cock wrote:
> Hello all,
>
> Good news - automated testing on the Galaxy Tool Shed
> seems to be mostly working again (after a period of trouble
> in the New Year). Thanks Dave B. et al, I'm sure this has
> been a lot of effort behind
Hi Björn,
Command line arguments are often case sensitive
(e.g. samtools switches), but are Galaxy parameter
names?
Peter
On Sat, Feb 28, 2015 at 9:11 PM, Björn Grüning
wrote:
> Hi all,
>
> we are planning to work on a project to implement a Galaxy fuse based
> shell. Probably starting with the
On Tue, Mar 3, 2015 at 5:32 PM, Dooley, Damion wrote:
> Ok, thanks Peter for the detailed feedback, change recommendations,
> and your work detailing all the NCBI Blast fields and quirks over time!
>
> The columns 25 and 26 stem from my predecessor's version of the
> code which predates blast 2.28
Hi all,
I was just surprised to find what I consider to be a major bug in
fasta_to_tabular_converter.py used to convert FASTA into tabular.
Consider this toy example:
>alpha
ACGTAC
>beta
AGTGTA
>gamma with some description
AGGTACCA
What the converter gives is two columns
Hello all,
I'm hoping to construct a workflow which produces a simple tally table
(using the "Count1" tool, "Count occurrences of each record", which is
still shipped with the Galaxy core) and then draws this as a Pie Chart.
1. Using "Count1", generate tally table (a simple two column tabular fil
On Tue, Mar 10, 2015 at 11:24 AM, Peter Cock wrote:
> Hello all,
>
> I'm hoping to construct a workflow which produces a simple tally table
> (using the "Count1" tool, "Count occurrences of each record", which is
> still shipped with the Galaxy core) a
On Fri, Mar 13, 2015 at 12:23 AM, Martin Čech wrote:
> Your tutorial looks great Damion! Thank you for sharing.
>
> I am not sure about the vocabulary you are trying to estabilish though
> (update vs revision). I understand what you mean but I would just stick with
> 'If the tool changed behavior
On Fri, Mar 13, 2015 at 3:31 PM, Carl Eberhard wrote:
> In short:
>
>>
>> Question: How can I "save" a static snapshot...?
>
> You can't yet.
>
>> Question: If so, can I then ...recreate the pie chart?
>
> No, not yet.
>
> Overall, these are features that we definitely want and we are working
> to
On Tue, Mar 17, 2015 at 1:20 PM, Peter Briggs
wrote:
> Hello
>
> Apologies as this seems to be quite a frequent question (and I may have
> missed something) however: are the tool tests being executed on the main or
> test toolsheds at the moment?
>
> The most recent tests results that I can find f
Thanks Jen & the whole Galaxy team.
I'm slightly disappointed the four digit year lobby group (.mm)
lost out to the yy.mm faction, but overall I'm very glad to see Galaxy
finally has real version numbers :)
Regards,
Peter
On Tue, Mar 17, 2015 at 2:37 PM, Jennifer Hillman-Jackson
wrote:
>
On Wed, Mar 18, 2015 at 10:13 AM, Peter Briggs
wrote:
> Hello Peter C.
>
> Thanks for your comments and advice Ironically after I sent that email the
> tests for the next tool I looked at in the toolshed had been run in the past
> couple of days.
That's good. I can also confirm that the Test Tool
18, 2015 at 1:46 PM, Dave Bouvier wrote:
> Gentlemen,
>
> The issue with the nightly testing was due to a stalled test run blocking
> subsequent tests. I've cleared out that blockage and a manual test run
> appears to have completed successfully, as should future automated test
&
Hello all,
I'm trying to install the intersect tool from the main Tool Shed,
https://toolshed.g2.bx.psu.edu/view/devteam/intersect
One of the dependencies fails to install, with the cryptic message
"Initializing repository installation failed [OK]":
https://toolshed.g2.bx.psu.edu/view/devteam/p
Hi Dave,
Can you check for stalls on the following repositories please?
They've not been tested for nearly two months:
https://toolshed.g2.bx.psu.edu/view/peterjc/clinod
Last tested 2015-01-29, Exception: Job in error state.
https://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
Last tested 2015-0
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock wrote:
> On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock wrote:
>> Hi all,
>>
>> I have a query about a failing tool test on the Tool Shed, where it
>> seems Galaxy is trying to convert both the expected BAM output
>> and t
ed.g2.bx.psu.edu/view/peterjc/mummer
I have not yet spotted any pattern in this division.
(However this is clearly not linked to the test expect_failure
test I'd added to the sample_seqs tool, as I speculated last
week.)
Regards,
Peter
On Wed, Mar 18, 2015 at 2:14 PM, Peter Cock wrote:
> Hi
On Mon, Mar 23, 2015 at 1:07 PM, John Chilton wrote:
> It seems to be happening during upload - so it is not unsurprising
> that this error would affect multiple tools. I have checked out the
> exact revision registered in the tests and the uploads seem fine to
> me.
You mean during the test-data
On Mon, Mar 23, 2015 at 1:41 PM, John Chilton wrote:
> Hey Peter,
>
> Thanks for continuing to apply pressure on these issues. I have
> pushed some logging into Galaxy's development branch
> (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d)
> that should m
On Mon, Mar 23, 2015 at 9:54 AM, Peter Cock wrote:
> Hi Dave,
>
> Can you check for stalls on the following repositories please?
> They've not been tested for nearly two months:
>
> https://toolshed.g2.bx.psu.edu/view/peterjc/clinod
> Last tested 2015-01-29, Exc
Hi all,
Unfortunately it appears that the new-look check box controls are wrongly
defaulting to ticking the first item rather than following the defaults given.
This is a recent regression which I noticed on updating our production Galaxy
to the 15.03 release which included a number of visual sty
On Fri, Mar 27, 2015 at 6:14 PM, Aysam Guerler wrote:
> A fix for this is on the way.
>
Thanks - if it can be applied on top of 15.03 that would be a bonus.
Peter
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Hi all,
I was testing a new workflow which I developed on the current
stable release, Galaxy 15.03, and uploaded to the Tool Shed
yesterday:
https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species
http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species
I then
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock wrote:
> ...
>
> Summary: Workflow requesting key entry "xxx" from example.loc
> (a) example.loc empty, gets empty path, fails cleanly.
> (b) example.loc contains xxx, gets correct path, works.
> (c) example.loc non empty bu
On Tue, Mar 31, 2015 at 12:04 PM, Peter Cock wrote:
> On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock
> wrote:
>> ...
>>
>> Summary: Workflow requesting key entry "xxx" from example.loc
>> (a) example.loc empty, gets empty path, fails cleanly.
>> (
l), and I’d consider it a pretty
> significant bug for reproducibility, etc.
>
> Thanks,
>
> Dan
>>> On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock
>>> wrote:
>>>> ...
>>>>
>>>> Summary: Workflow requesting key entry "xxx"
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