On Thu, Jul 17, 2014 at 2:43 PM, Calogero Zarbo wrote:
> Ok, thanks for the the tip.
>
> I changed the XML to this one:
>
>
>
> label="Training Dataset extracted from ${input_dataset.name}">
>
> format="fbk-svm-dataset"/>
>
>
>
>
>
On Thu, Jul 17, 2014 at 4:31 PM, Eric Rasche wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> For those reading this thread from the future, there's a secret to
> adding completely new datatypes locally (and not through a toolshed).
>
> You have to manually edit lib/galaxy/datatypes/re
On Thu, Jul 17, 2014 at 5:45 PM, Björn Grüning
wrote:
> Hi,
>
> I think you are right John. Datatypes have many issues in that regard as I
> can tell, from a few bug reports. Imho datatypes should be handled like
> "Tool dependency definitions". There should be only one "installable
> revsion".
>
On Thu, Jul 17, 2014 at 5:55 PM, Eric Rasche wrote:
>
> Not a problem Peter, it's a somewhat subtle bug to have, and there isn't
> a lot of documentation on the wiki about writing new datatypes (though I
> plan to fix that soon).
>
> That particular error message could stand to be a bit more expli
On Thu, Jul 17, 2014 at 6:10 PM, Björn Grüning
wrote:
>
> ... but the problem will stay the same ... one [datatype definition]
> repository
> can have multiple versions ...
>
I like your idea that like tool dependency definitions, this should be a special
repository type on the ToolShed:
Earlie
On Thu, Jul 17, 2014 at 6:28 PM, Eric Rasche wrote:
>> Am 17.07.2014 18:51, schrieb Peter Cock:
>>>
>>> One reason I have been meaning to do some of these is familiarity with
>>> many of these formats from looking after/writing parsers in Biopython.
>
> Pet
that are removed in a later changeset revision would
> no longer be available.
>
> Greg
>
> On Jul 17, 2014, at 1:30 PM, Peter Cock wrote:
>
>> On Thu, Jul 17, 2014 at 6:10 PM, Björn Grüning
>> wrote:
>>>
>>> ... but the problem will stay the same ..
On Thu, Jul 17, 2014 at 7:19 PM, Eric Rasche wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Thanks to everyone for their assistance in my adventure of custom local
> datatypes. In response to this, I've added a new wiki page with a basic
> MWE/tutorial on adding datatypes. A complete
You could do something like that, and we already have
Biopython packages in the ToolShed which can be listed
as dependencies :)
However, some things like GenBank are tricky - in order
to tolerate NCBI dumps the Biopython parser will ignore
any free text before the first LOCUS line. A confusing
sid
Hi Renato,
You probably need to look at overriding the display_data method
in your subclass, see here for a simple example to render a
binary composte file type as a simple text caption:
https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py
You can also override
On Thu, Jul 17, 2014 at 8:20 PM, Eric Rasche wrote:
> On 07/17/2014 02:11 PM, Peter Cock wrote:
>> You could do something like that, and we already have
>> Biopython packages in the ToolShed which can be listed
>> as dependencies :)
>>
>
> If my module depends o
On Fri, Jul 18, 2014 at 4:21 PM, Eric Rasche wrote:
> On 07/18/2014 09:49 AM, John Chilton wrote:
>> My understanding of the code is that tool shed dependencies (or local
>> dependencies) will not be available to tool shed datatypes (for
>> sniffing for instance). Sorry.
>
> I figured as much, not
On Fri, Jul 18, 2014 at 5:14 PM, Dave Bouvier wrote:
> John, Peter,
>
> The buildbot builders are already using the api interactor for both
> functional tests and the install and test framework.
>
> --Dave B.
Great news.
When did that happen? Did it cause any regressions (and
can/did you flag
On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning wrote:
> Hi,
>
> single datatype definitions only work if you haven’t defined any converters.
> Let's assume I have a datatype X and want to ship a X -> Y converter (Y -> X
> is also possible), we will end up with a dependency loop, or? The X
> reposi
On Mon, Jul 21, 2014 at 6:51 PM, Eric Rasche wrote:
> Currently the checkout options consist of hg clones, and archives that
> mercurial produces.
>
> Having pulled or cloned galaxy a few times lately, I'm wondering if anyone
> would have a use for a once-run galaxy instance in an archive? I.e., I
On Tue, Jul 22, 2014 at 1:15 PM, Eric Rasche wrote:
> Hi Peter,
>
> On July 22, 2014 3:15:41 AM CDT, Peter Cock wrote:
>>
>>Given how close you can get now for minimal effort,
>>this seem unnecessary.
>>
>>http://blastedbio.blogspot.co.uk/2013/09/using-
Set yourself as an administrator, and you can import the files
from disk (and link to them if you wish to avoid a copy) as part
of a data library. See:
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
Peter
On Tue, Jul 22, 2014 at 3:52 PM, Mark Lindsay wrote:
> Apologies
On Tue, Jul 22, 2014 at 7:41 PM, Eric Rasche wrote:
> John,
>
> How are those generated? Would you be amenable to scripting that
> portion and running it once a month? (...say in a cron job, with a
> passwordless ssh key so you never have to touch it again)
>
> Cheers,
> Eric
How to generate it w
On Wed, Jul 23, 2014 at 10:47 AM, Ulf Schaefer wrote:
> Dear all
>
> I have several smallish BLAST databases that I would like to provide in
> a data library. I create them in a history with the makeblastdb tool and
> them try to add them to the library. I see that for each blast db there
> is an
Interesting hypothesis - you may well be right.
Galaxy guys - who is the expert to talk to on this and/or where
in the code should we be looking?
Thanks,
Peter
On Wed, Jul 23, 2014 at 11:22 AM, Ulf Schaefer wrote:
> Dear Peter
>
> Thanks for your reply.
>
> I can import an html report (e.g. Fa
On Wed, Jul 23, 2014 at 2:42 PM, John Chilton wrote:
> Problem with automation is I could create dozens of templates over the
> next several years and consume less time in aggregate than it would
> take me to automate this. Nonetheless, there is a documentation
> component here that is important s
On Thu, Jul 24, 2014 at 2:50 PM, Nate Coraor wrote:
> On Jul 23, 2014, at 6:42 AM, Peter Cock wrote:
>
>> Interesting hypothesis - you may well be right.
>>
>> Galaxy guys - who is the expert to talk to on this and/or where
>> in the code should we be looking?
&
On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer wrote:
> Dear Nate, dear Peter
>
> Sorry for the delay in replying.
>
> I can import both HTML and blastdb from a history to a data library. If
> I try to get the data out of the library into anothre history, I am
> successful for the html but not for
On Mon, Jul 28, 2014 at 11:03 AM, Wolfgang Maier
wrote:
> Dear all,
>
> I noticed that with params of type "text" Galaxy seems to replace certain
> characters before passing them to the shell. As examples, it changes "@" to
> "__at__", "}" to "__cc__" and "\" to "X".
> Is this the standard behavio
On Mon, Jul 28, 2014 at 12:23 PM, Wolfgang Maier
wrote:
> On 28.07.2014 12:22, Peter Cock wrote:
>>
>> This is standard behaviour to prevent special characters being used
>> to construct malicious command lines. It can be configured within
>> your tool definition usin
Hi all,
I'm not sure when this started (having hardly looked at my Tool Shed
test results since GCC2014), but I think this is a fairly recent problem
with my BLAST RBH tests failing (which has held me back from posting
this to the main Tool Shed).
This could be some silly mistake in my tar-ball,
Hi John,
Following the work at the BOSC 2014 CodeFest to support
embedded citations within Galaxy Tool XML files [1], and your
work adding this to the BLAST tools as an example [2], I tried
uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary
On Wed, Jul 30, 2014 at 11:52 AM, Ulf Schaefer wrote:
> Dear Nate, dear Peter
>
> Again, sorry for the delay in replying.
>
> Yes I can. It looks like this
>
> [galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat
> [galaxy@srv ~]$ ls /galaxy/database/files/081/dataset_81002_files/
> bl
code should be fixed with
> https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f
> - it is in next-stable so I think the tool shed should pick up that
> fix at next tool shed update.
>
> -John
>
> On Wed, Jul 30, 2014 at 5:43
be Greg will weigh in on whether that makes
>> sense.
>>
>> -John
>>
>> On Wed, Jul 30, 2014 at 7:14 AM, Peter Cock
>> wrote:
>>> Thanks John - is there any point/benefit to re-uploading
>>> my tool once the fix is live on the Tool Shed
se it is defined as a
> repository dependency, not a tool dependency. I would recommend replacing
> the repository dependency in the blast_rbh repository with a tool dependency
> definition that references package_blast_plus_2_2_29.
>
> --Dave B.
>
> On 07/30/2014 05:27 AM, Peter Cock wr
On Thu, Jul 31, 2014 at 5:21 PM, bjoern.gruen...@googlemail.com
wrote:
> Hi Peter,
>
>
> 2014-07-31 10:57 GMT+02:00 Peter Cock :
>
>> Hi Dave,
>>
>> You are right that on closer inspection I've mixed tool_dependencies.xml
>> and repository_dependenci
Hi Mert,
Most of the Galaxy tools dealing with tables of data use "tabular"
format (tab separated variables), not csv (comma separated
variables). CVS is a horrible horrible mess of formats, see e.g.
http://tburette.github.io/blog/2014/05/25/so-you-want-to-write-your-own-CSV-code/
Also beware tha
On Mon, Aug 4, 2014 at 4:28 PM, Eric Rasche wrote:
> Hi Peter,
>
> On 08/04/2014 09:25 AM, Peter Cock wrote:
>> Hi Mert,
>>
>> Most of the Galaxy tools dealing with tables of data use "tabular"
>> format (tab separated variables), not csv (comma separate
Hi Geert,
Which tool is this?
Peter
On Thu, Aug 7, 2014 at 9:00 AM, Geert Vandeweyer
wrote:
> Hi,
>
> I get an installation error on the python 2.7 package in the test toolshed.
> I used the 'contact owner' function, but wanted to mention it here too, as
> there hasn't been reaction so far. Sor
On Thu, Aug 7, 2014 at 4:29 PM, Sajdak, Doris wrote:
> I’m in an odd situation: I was given an older version of Galaxy with
> additional tools built into it by a new faculty member. He brought this
> from his former institutions and wanted us to run his Galaxy instance on our
> systems. We don’
Hi all,
I've just uploaded a simple sequence composition tool to the
Test Tool Shed:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition
https://github.com/peterjc/pico_galaxy/commit/45669446f5a14fd90a8a0d9d7430499de2fb3493
This accepts multiple input in FASTA, FASTQ, or SFF format -
On Tue, Aug 12, 2014 at 5:31 PM, John Chilton wrote:
> Fun question! I have opened a pull request with my answer -
> https://bitbucket.org/galaxy/galaxy-central/pull-request/457/allow-cheetah-tool-templates-to-reason/diff.
>
> There are three different hacks you can use right now... here is a
> di
On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche wrote:
> Hi Peter,
>
> I'm working on composite datatypes now (for PacBio SMRT cells). In the
> datatype I know I'll have files with variable names (e.g. .1, .2, .3) and
> after using the blast datattype as reference material, I noticed that you
> had c
On Mon, Jul 28, 2014 at 9:43 AM, Peter Cock wrote:
> On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer wrote:
>> Dear Nate, dear Peter
>>
>> Sorry for the delay in replying.
>>
>> I can import both HTML and blastdb from a history to a data library. If
>> I try
Hi all,
Are the main and test tool-sheds currently meant to
be running the tool functional tests every 48 hours?
I created and updated these repositories last week,
but they have yet to be tested:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition
https://testtoolshed.g2.bx.psu.edu/
On Mon, Aug 18, 2014 at 11:16 AM, Peter Cock wrote:
> Hi all,
>
> Are the main and test tool-sheds currently meant to
> be running the tool functional tests every 48 hours?
>
> I created and updated these repositories last week,
> but they have yet to be tested:
>
&
On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic
wrote:
>
> Mira doesn’t work on Galaxy. This is the log message I receive.
>
> Tool: Assemble with MIRA v3.4
> Name: MIRA log
> Created: Fri Aug 22 00:24:38 2014 (UTC)
> Filesize: 0 bytes
> Dbkey: ?
> Format: txt
> Galaxy Tool Version: 0.0.10
> T
On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic
wrote:
> Hi Peter,
>
> I don¹t know what the stdout and stderr information was. I click on it but
> nothing comes up.
>
> I installed from the main toolshed:
> http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
> Yes, I did use the test to
On Fri, Aug 22, 2014 at 8:00 PM, Peter Cock wrote:
> On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic
> wrote:
>
>> Also I can’t install Mira 4. This is the message I receive.
>> Any suggestions.
>
> Getting "Internal Server Error" is unhelpful - I can
Do you mean a SAM/BAM file sorted by read name?
If so, try samtools sort -n ... instead.
Peter
On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott
wrote:
> Hello all,
>
> My users are trying to use a tool called bismark and it requires an unsorted
> SAM file for one of its steps
>
> Previous st
96 separate files to process hence the desire to use a workflow.
>
> Regards,
>
> Alistair
>
>
>
>
> -Original Message-
> From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
> Sent: Thursday, 28 August 2014 2:27 PM
> To: Alistair Chilcott
> Cc: galaxy-dev@
On Fri, Aug 29, 2014 at 11:43 PM, Lukasse, Pieter wrote:
> So I need to refresh on changeI see that if I have a conditional item in
> my form, this causes a refresh of the page and a (re)evaluation of my
> dynamic_options methodsso I could misuse this “feature”.
This is deliberate, althou
On Sat, Aug 30, 2014 at 11:17 AM, Melissa Cline wrote:
> Hi folks,
>
> I'm attempting something that should be straightforward, but it's not. I
> have a tool that runs a JAR file, which I have bundled with the tool. I
> simply want to run the JAR file. And to paraphrase Thomas Edison, I've
> tr
You might be able to do this by accepting a collection of
SAM/BAM files as input instead. This is a quite new feature
in Galaxy, see:
https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution
Peter
On Wed, Sep 3, 2014 at 10:00 AM, Philippe Moncuquet
wrote:
> Hi,
>
> I am trying to writ
Hi all,
I'm wondering why my samtools_depad repository tests have
failed, and since I have not changed this recently presume this
is due to a Galaxy change or general TestToolShed problem
not specific to my tool:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
Tests that failed
To
On Wed, Sep 10, 2014 at 7:55 PM, Nate Coraor wrote:
> Hi Peter,
>
> This was due to a bug I introduced last week, which I've just fixed in
> d1f6d05. Sorry for the trouble.
>
> --nate
Thanks - I'll check back in a day or two once the tests have
run again.
Peter
__
On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison wrote:
> The stderr and stdout is empty, according to galaxy.
>
> here is paster.log output for quikr when i run it.
>
>
> galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user
> == "user" quikr -v -k 0 -s
> /data/galaxy/gal
Hi Calvin,
The "extension" is really the Galaxy datatype name, so
put "quikrdb" here. The actual filename on disk will be *.dat
once loaded into Galaxy.
More examples, e.g.
https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/datatypes_conf.xml
Peter
On Fri, Sep 12, 201
On Fri, Sep 26, 2014 at 3:01 PM, Nikos Sidiropoulos
wrote:
> Hi all,
>
> In a tool that I am writting I want to pass an input parameter value
> (string) into the output file's metadata. Meaning that one of the tool
> parameters is a barcode signature, 'NNWTGXN' for example. I want that
> attribute
On Tue, Sep 30, 2014 at 4:34 PM, David Hoover wrote:
> Why isn't there a datatype for a directory of files? This seems like
> such a simple thing. If an executable generates or expects a
> directory as its input or output, why must a fancy complicated
> composite datatype be created to handle th
On Tue, Oct 7, 2014 at 1:47 AM, Isabelle Phan
wrote:
> Hello,
>
> I installed clustalomega from the galaxy main toolshed using the admin
> interface of our local galaxy install.
>
> When I run the tool, I get this message:
>
>
> Dataset generation errors
> Dataset 55: co_alignment.fasta
>
On Wed, Oct 8, 2014 at 12:49 AM, Dave Clements
wrote:
> Hi All,
>
> The October Galaxy newsletter went out a week ago. Buried at the bottom is
> this
>
> 36 new ToolShed repos
--> https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions
> which lists repositories that have be
Hi all,
>From the "new tools" information Dave Compiled for the last Galaxy Update
https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions
I had a look at galaxyp's "filter_by_fasta_ids: Extract sequences from a
FASTA file based on a list of IDs" tool:
https://toolshed.g2.bx.p
On Wed, Oct 8, 2014 at 11:20 AM, Stef van Lieshout
wrote:
> Anyone else getting this when trying to upload to a testtoolshed repos?
> I'm using the "upload files to repository" function in "repository
> actions" and get a blank page with "internal server error".. Worked fine
> yesterday.
>
> Ciao,
OK good - my issue with the ToolShed work now too :)
On Wed, Oct 8, 2014 at 11:44 AM, Stef van Lieshout
wrote:
> Ok, works for me again. Just a little hiccup I guess...
>
> Stef
>
> - Original message -
> From: Peter Cock
> To: Stef van Lieshout
> Cc: Galaxy Dev
On Wed, Oct 8, 2014 at 9:22 AM, Peter Cock wrote:
> Hi all,
>
> From the "new tools" information Dave Compiled for the last Galaxy Update
> https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions
> I had a look at galaxyp's "filter_by_
On Thu, Oct 16, 2014 at 11:05 PM, Wolfgang Maier
wrote:
> Hi,
>
> this is just to make sure: the GALAXY_SLOTS environmental variable set by
> Galaxy when running tools will always be a number >= 1 with 1 being the
> default if nothing else is configured in the job runner settings ?
>
> Correct ?
>
Hi Matthias,
Can you file an issue here about adding this here please?
https://github.com/peterjc/galaxy_blast
Thanks!
Peter
On Tue, Oct 21, 2014 at 10:36 AM, Matthias Enders
wrote:
> Hello all,
>
> I use the ToolShed NCBI Blast+ Wrappers
> (https://toolshed.g2.bx.psu.edu/repository?repositor
, Oct 22, 2014 at 6:57 AM, Matthias Enders
wrote:
> Hi Peter,
>
> I added a new Issue, hope everything is correct.
>
> Kind regards,
> Matthias Enders
>
>
> -Ursprüngliche Nachricht-
> Von: Peter Cock [mailto:p.j.a.c...@googlemail.com]
> Gesendet: Tuesday, Oc
On Fri, Oct 24, 2014 at 10:17 PM, Lukasse, Pieter wrote:
> Hi Bjoern, John,
>
> thanks, this worked!
>
> So: I have to add a repository dependency to my tool_dependencies.xml
> file and NOT to my repository_dependencies.xmlI must say it is somewhat
> confusing. Somehow I had this idea that too
Hi all,
I have a suite_config.xml file in one of my Tool Shed packages,
but I am unclear if this is still used, or simply a legacy from the
old pre-hg-based Tool Shed? e.g.
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/suite_config.xml
My understanding was this allowe
Hi all,
I'm getting the following exception in a failing unit test:
https://travis-ci.org/peterjc/pico_galaxy/builds/39398677
Testing this tool (where two of the three near identical tests passed):
https://github.com/peterjc/pico_galaxy/blob/dd03346710e6a46cb6ec9dda1eed23d5fd301d03/tools/mummer/m
Hi all,
It seems the ToolShed now uses roles for granting admin rights...
but still has the old "Grant authority to make changes" feature?
I just hit a possible glitch here - I wanted to create a new repo
under the "iuc" user, edit the admin settings, then log in as my
normal personal account and
I have "solved" this by commenting out the apparently harmless test:
https://github.com/peterjc/pico_galaxy/commit/f3d4261846566a86f9c85a158fb95877ca8bc7c5
Peter
On Wed, Oct 29, 2014 at 5:39 PM, Peter Cock wrote:
> Hi all,
>
> I'm getting the following exception in a fa
On Sat, Nov 1, 2014 at 2:30 AM, Ross wrote:
> Hi, Bruno.
> As Björn points out, cross-toolshed dependencies aren't currently supported
> but exporting (eg) package_r_3_1_1 as a capsule (make sure to include ALL
> dependencies) from one toolshed and importing that capsule into your own
> local tool
Hello all,
I am currently hoping to review the automated test results for
some repositories which I have recently updated, in one case
for dependency handling, the other functional changes:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer
https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi
Hi all,
I'm running galaxy-central as my development server, and noticed what
to me is a regression with repeat parameters,
e.g.
https://github.com/peterjc/pico_galaxy/blob/master/tools/clc_assembly_cell/clc_mapper.xml
Read group:
[+ insert read group]
* 1: Read Group
* 2: Read Group
which on
Hello all,
Galaxy currently requires samtools on the $PATH in order to sort
and index BAM files automatically, and samtools 0.1.19 works fine.
Unfortunately later versions of samtools index have a regression:
https://github.com/samtools/samtools/issues/199
This has caught several people out alre
should normally be 0.1.19 or older, due to the not-yet-implemented
> handling of bam_index_build and other potential regressions that could be
> uncovered in the future.
>
>--Dave B.
>
>
> On 11/03/2014 01:52 PM, Peter Cock wrote:
>>
>> Hello all,
>>
>>
results from the Tool Sheds ...
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-November/020792.html
Thanks,
Peter
On Tue, Nov 4, 2014 at 8:38 AM, Peter Cock wrote:
> OK, so this should work then... :)
>
> Thanks Dave,
>
> Peter
>
> On Mon, Nov 3, 2014 at 7:06 PM, Dave Bou
Hi all,
I'm looking for a little advice on the pre-existing SAM/BAM filtering
tools already in the Galaxy Tool Shed (to avoid reinventing the wheel).
As I mentioned on another thread, I'm working on a wrapper for the
"samtools bam2fq" command (targeting samtools 1.1 which fixed
some bugs in this
On Tue, Nov 4, 2014 at 2:44 PM, Peter Cock wrote:
> Hi all,
>
> I'm looking for a little advice on the pre-existing SAM/BAM filtering
> tools already in the Galaxy Tool Shed (to avoid reinventing the wheel).
>
> As I mentioned on another thread, I'm working on a wrappe
>
> --Dave B.
>
>
> On 11/03/2014 05:51 AM, Peter Cock wrote:
>>
>> Hello all,
>>
>> I am currently hoping to review the automated test results for
>> some repositories which I have recently updated, in one case
>> for dependency handling, the o
oes not relocate on the
> screen after adding new repeat blocks.
>
> Thanks,
> Sam
>
> On Mon, Nov 3, 2014 at 7:25 AM, Peter Cock
> wrote:
>>
>> Hi all,
>>
>> I'm running galaxy-central as my development server, and noticed what
>> to me i
Hello all,
Because Galaxy uses the upload tool internally for the inputs for
function tests, it is possible to bundle gzipped versions of test
inputs which saves space. For example,
https://github.com/peterjc/pico_galaxy/blob/master/tools/clc_assembly_cell/clc_mapper.xml
However, what I have jus
guess we could
> try something like compare the contents - if not matching and the test
> target is compressed - decompress and retry. I've created a Trello
> card - https://trello.com/c/ebdBkezi.
>
> Thanks for the suggestion,
> -John
>
> On Thu, Nov 6, 2014 at 12:32 PM, Pete
Hi Sam,
On Thu, Nov 13, 2014 at 6:25 AM, Aysam Guerler
wrote:
> Hey Peter,
>
> I have modified the data selectors appearance by adding a single select
> field as default option. It resembles the previous functionality now and I
> think its an improvement.
>
Great. I won't be able to try this u
Hello all,
There looks to be an egg problem with the latest galaxy-central,
here are excepts from a failed Galaxy install on my TravisCI test
setup,
https://travis-ci.org/peterjc/pico_galaxy/builds/41233860
Here's another project build with the same error:
https://travis-ci.org/peterjc/galaxy_bla
On Mon, Nov 17, 2014 at 7:23 PM, John Chilton wrote:
> Ummm... I think it is that the VM started shipping with an
> incompatible paramkio.
>
> [...]
>
> Anyway - planemo's TravisCI integration tests Galaxy in a virtualenv
> and it works fine [...]
That's a useful workaround, but a virtualenv is n
On Nov 18, 2014 7:26 AM, "John Chilton" wrote:
>
> I will admit to not actually understanding Galaxy's dependency management
> but I think virtualenv is exactly the advice people who do understand it
> give
> http://dev.list.galaxyproject.org/Local-installation-problem-td4662627.html.
> It is a wi
On Tue, Nov 18, 2014 at 1:24 PM, Peter Cock wrote:
> On Nov 18, 2014 7:26 AM, "John Chilton" wrote:
>>
>> I will admit to not actually understanding Galaxy's dependency management
>> but I think virtualenv is exactly the advice people
On Tue, Nov 18, 2014 at 5:51 PM, Nate Coraor wrote:
> Peter,
>
> Unless you've made modifications to Galaxy that depend on external
> libraries, switching to a virtualenv for the server itself should be
> pretty safe. Tools themselves can still run without using the/any
> virtualenv, if desired.
>
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 night.
>
> e.g. My new
On Wed, Nov 19, 2014 at 9:36 AM, Peter Briggs
wrote:
> Hello
>
> I'm trying to make a new repository on the public toolshed at
> https://toolshed.g2.bx.psu.edu/
> but I keep getting the "internal server error" page.
>
> I was also unable to log out, or even to see the front page when trying to
> a
Thanks - uploading tar-balls to the Test Tool Shed is working again :)
Peter
On Wed, Nov 19, 2014 at 2:34 PM, Nate Coraor wrote:
>
> Hi all,
>
> Sorry for the service interruption. The Tool Shed should be back now,
> and the underlying disk usage problem has been alleviated, so it
> shouldn't oc
Hi John, Sam,
I've not done it yet, but was hoping to implement uploading of
BLAST databases at some point - mainly for use within the
test framework, rather than expecting it to be useful for the
end user.
Is the issue here uploading an archive (e.g. .zip or .tar.gz) or
offering a way to pick mu
ted in the next run.
>
> -John
>
>
> On Wed, Nov 19, 2014 at 4:48 AM, Peter Cock wrote:
>>
>> Hi Dave,
>>
>> Any progress? All the following seem to have been tested
>> in the last few days on the TestToolShed, but failed with
>> "Exception: H
On Fri, Jul 29, 2011 at 1:01 AM, Ka Ming Nip wrote:
> My jobs have this problem when the command for the tool is wrapped by the
> stderr wrapper script.
>
> Ka Ming
Which stderr wrapper script? I think there is more than one...
I've also had this error message (I'm currently working out how to
Hi all,
I've run into some file permissions problems as part of using the same
mapped directory
on both the Galaxy server and our cluster. In the process I wrote the
following patch which
fixes the following bug - where Galaxy seems to leave the job in the
pending state:
galaxy.jobs INFO 2011-07-
Hi all,
In my recent email I mentioned problems with our setup and mapped drives. I
am running a test Galaxy on a server under a CIFS mapped drive. If I map the
drive with noperms then things seem to work with submitting jobs to the cluster
etc, but that doesn't seem secure at all. Mounting with s
On Saturday, July 30, 2011, Shantanu Pavgi wrote:
>
> The -V option is not for verbose mode but for exporting your
> shell environment. Refer to qsub manual for details:
> "Specifies that all environment variables active within the
> qsub utility be exported to the context of the job."
> We are
Note: Local install questions are normally directed to the galaxy-dev
list (CC'd)
rather than galaxy-user
On Mon, Aug 1, 2011 at 3:21 PM, Joseph Hargitai
wrote:
> Enis,
>
> a few things we came across:
>
> a, local install
>
> R - not the correct download url,
Which URL are you talking about? Th
Hi Jeseph,
I see now you are talking about Enis' code for automated building of
virtual machine
Galaxy images, https://bitbucket.org/afgane/mi-deployment/src -
mentioned briefly
here: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
I know very little about this area of Galaxy - we install any
Dear all,
I've just uploaded my Galaxy wrapper for command line NoD (clinod) to
the Galaxy tool shed (under the Sequence Analysis category):
http://usegalaxy.org/community
NoD is from the Barton group at the University of Dundee, and does
Nucleolar localization sequence (NoLS) prediction. There i
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