Hello all,
Marco, Jon and I are going to try to get together during GCC2015
for a BOF (a Birds of a Feather informal meeting) to talk about
Galaxy parallelisation (and collections). We've not yet picked a time,
but details should be on the wiki shortly...
Hi Damion,
The NCBI have a bug here - if it is just a warning, it shouldn't
say Error. We had something similar before:
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA
modifier(s) found because the input was not expected to have any.
In that case the NCBI fixed it, see
On Sat, Jul 4, 2015 at 5:09 PM, Dooley, Damion damion.doo...@bccdc.ca wrote:
Sure I could probably step up to the plate on that one. I haven't
reported it to NCBI - it didn't twig that this was an exit code 0 .
I'll sneak it into BOSC codefest maybe!
d.
What is the error code? It might
Hi Ryan,
Something very handy for tool developers running functional tests
is if the environment variable GALAXY_TEST_NO_CLEANUP
is set, run_tests.sh shouldn't remove the test output.
This is great when debugging why a test is failing.
Peter
On Fri, Jun 12, 2015 at 4:29 PM, Ryan G
.
On Fri, Jun 12, 2015 at 12:03 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi Ryan,
Something very handy for tool developers running functional tests
is if the environment variable GALAXY_TEST_NO_CLEANUP
is set, run_tests.sh shouldn't remove the test output.
This is great when debugging
Hi all,
Searching on the main Tool Shed for fastqc gives two conflicting
tools, an older version from the IUC, and a newer version from
the devteam.
If no one objects, I would like to mark the older IUC entry as
deprecated, and edit the description to refer to the more up to
date devteam entry
Hi all,
Looking at https://toolshed.g2.bx.psu.edu/ logged in a peterjc, the
Repositories I Can Change / Latest revision: installation errors
listing ought to be empty, but is very long (perhaps all my tools?).
The individual tools show things like:
Galaxy itself will call samtools index on BAM files, so
they should be there on disk already, See for example:
https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_idxstats/samtools_idxstats.xml
On Wed, May 20, 2015 at 3:39 PM, Eric Rasche e...@tamu.edu wrote:
Howdy Devs,
I'd like to see BioPython added as an egg. I mentioned this on IRC, but it
sort of fell off. A couple of users spoke positively about having it as a
dependency.
Do any of the devs have further opinions on this?
On Mon, May 18, 2015 at 1:55 PM, Brian Haas bh...@broadinstitute.org wrote:
Thanks, Peter! I've verified that I can get your code to work - bundling
the composite files. I'll keep plugging away at my little example and see
if I can figure out what's going awry.
more later. Thx again!
Hi Brian,
Your original email with attachments has made it to the list now,
http://dev.list.galaxyproject.org/difficulty-creating-composite-data-type-tp4667193.html
Title: difficulty creating composite data type
Peter
On Mon, May 18, 2015 at 2:25 PM, Brian Haas bh...@broadinstitute.org wrote:
On Sun, May 17, 2015 at 5:44 PM, Brian Haas bh...@broadinstitute.org wrote:
Greetings.
Does anyone per chance have a simple working example of using composite data
types? I've gotten as far as I can with the galaxy documentation, and I
can't seem to get the additional files bundled into an
On Fri, May 8, 2015 at 6:55 PM, Nicola Soranzo nsora...@tiscali.it wrote:
The problem is not in the Cheetah code, which does not get executed because
of the validation error.
I think this a Galaxy bug which tries to validate the parameter values but
interprets the value None of the
On Fri, May 8, 2015 at 3:05 PM, Peter Briggs
peter.bri...@manchester.ac.uk wrote:
Hello
I'm currently writing tests for a tool and think I've found a situation where
the behaviour of the boolean parameter type does not seem correct within the
test environment.
The tool defines the
Hi Roberto,
Given the way BAM indexing works, I see no reason to actually
split the BAM file at all - it seems like wasted disk IO.
Instead, can you split a BED file into sub-regions? This way
each child GATK job would look at the full BAM file but only for
a small region described in the split
On Wed, May 6, 2015 at 11:33 AM, Roberto Alonso CIPF ralo...@cipf.es wrote:
Hello,
I agree, what you say fits perfectly for GATK, but as I wanted to create a
more generic code I did it this way (also because I am a newbie in the
galaxy code and I didn't know so well how to implement this ).
Hi Carlos,
We're running Galaxy on CentOS 6.6, so that in itself shouldn't be a
problem. Most of the effort was sorting out shared storage with the
cluster, which in our case is managed with SGE (fairly commonly
used with Galaxy).
In reply to your thread last month David Trudgian said he was
Hi all,
I think this is the second time I've have the following error on
TravisCI (last time I reran a similar failure, and it worked). I've
not yet re-run the test so that you can see the full error log:
UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
Yes, for example:
https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml
Peter
On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Ryan
I guess you can work with filters, see:
good understanding of now. We've tried
a few different ideas for fixing it, (obviously none of which have worked,
yet), and I've been poking at a new fix this week.
-Dannon
On Wed, Apr 29, 2015 at 6:53 AM Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi all,
I think this is the second time
On Wed, Apr 29, 2015 at 4:40 PM, Roberto Alonso CIPF ralo...@cipf.es wrote:
Ok, no problems ;)
It is another PR, I think it is useful without the other PR, for example
when you map with BWA. The last PR will be like the next step, I mean for
example that you split a bam to do some calling or
On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman
simon.glad...@unimelb.edu.au wrote:
Hi dev,
Now that the code tagset is deprecated, how do we replace that
functionality. For example the get microbial data tool runs the script
listed in the code tagset to load the list of available microbe data
You probably need to set the stdio tag, since due to a
historical design choice by default any output on stderr
is treated as an error. See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Peter
On Tue, Apr 28, 2015 at 4:41 PM, Ryan G ngsbioinformat...@gmail.com wrote:
Hi - I
On Mon, Apr 27, 2015 at 5:23 PM, Christian Brenninkmeijer
christian.brenninkmei...@manchester.ac.uk wrote:
Hi All,
If there is a separate planemo mailing list please point me there.
Not that I am aware of, galaxy-dev seems fine.
I have been planing with planemo and find it a great tools.
Hi all,
I don't see tool README files on the main view of a repository
any more. Is this a recent regression?
e.g. https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools
and https://testtoolshed.g2.bx.psu.edu/view/bgruening/deeptools
should show the readme.rst file
e.g.
On Thu, Apr 16, 2015 at 1:59 PM, Christian Brenninkmeijer
christian.brenninkmei...@manchester.ac.uk wrote:
Hi,
I am a new galaxy developer playing with writing my first plugins
In my plugin xml configaration file:
I want to be able to increase the value of one parameter based on another
I just hit a problem installing package_bx_python_0_7 via the Admin GUI.
Name: bx-python
Version: 0.7.1
Type: package
Status: Error
Error: Error installing tool dependency bx-python version 0.7.1:
coercing to Unicode: need string or buffer, NoneType found
Name: galaxy-ops
Version: 1.0.0
Type:
Marten has added this to an existing issue - over zealous
over escaping due to a security fix:
https://trello.com/c/oX6i51Mn/2298-back-off-over-escaping
Thanks,
Peter
On Wed, Apr 8, 2015 at 5:13 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I just imported a workflow and noticed
On Mon, Mar 23, 2015 at 12:27 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
Now that you've fixed some of the test back log, the bad
news is this issue I reported last week appears to be a major
regression affecting multiple tools on the Test Tool Shed:
https://testtoolshed.g2
On Thu, Apr 2, 2015 at 10:02 AM, Nikhil Joshi najo...@ucdavis.edu wrote:
Hi all,
So in my wrapper for my trimming tool, sickle, I only allow fastq,
fastqsanger, fastqillumina, or fastqsolexa input data. However, if a
fastqsanger file's datatype has been erroneously changed to fastqcssanger,
On Wed, Apr 1, 2015 at 11:29 AM, Saket Choudhary sake...@gmail.com wrote:
On 1 April 2015 at 02:06, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchil...@gmail.com wrote:
I think it is probably a pair of bugs you are seeing:
...
The fix
Hello all,
I've been playing with the Tool Shed lately for publishing
Galaxy workflows - and realised the download process is
still very complicated, especially the final hurdle - importing
the workflow in order to actually use it.
For the following example I am starting from a clean state -
an
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock p.j.a.c...@googlemail.com 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 but lacks xxx
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
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
On Fri, Mar 27, 2015 at 6:14 PM, Aysam Guerler aysam.guer...@gmail.com 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
___
Please keep all replies on the list by using reply
.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 p.j.a.c...@googlemail.com
On Mon, Mar 23, 2015 at 1:41 PM, John Chilton jmchil...@gmail.com 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)
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock p.j.a.c...@googlemail.com 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
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
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]:
On Fri, Mar 13, 2015 at 12:23 AM, Martin Čech mar...@bx.psu.edu 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
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
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:
option value=std selected=TrueStandard 12 columns/option
option value=std+seqsStandard 12 columns +
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
bjoern.gruen...@gmail.com wrote:
Hi all,
we are planning to work on a project to implement a Galaxy fuse based
shell.
On Fri, Feb 27, 2015 at 10:36 PM, Dooley, Damion damion.doo...@bccdc.ca 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
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
On Fri, Feb 27, 2015 at 8:58 PM, Dooley, Damion damion.doo...@bccdc.ca 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
On Thu, Feb 26, 2015 at 2:43 PM, John Chilton jmchil...@gmail.com wrote:
Also not need to escape $__tool_directory__ (so use
$__tool_directory__ instead of \$__tool_directory__).
-John
If this was unclear, $VAR in the command XML fragment
is taken to be a Python variable available within
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton jmchil...@gmail.com 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
On Thu, Feb 26, 2015 at 2:24 PM, John Chilton jmchil...@gmail.com 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
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 p.j.a.c...@googlemail.com 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 up, having fixed
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon mike.t...@gmail.com 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
On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning
bjoern.gruen...@gmail.com 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
On Tue, Feb 24, 2015 at 2:57 PM, Dannon Baker dannon.ba...@gmail.com 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
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
On Tue, Feb 24, 2015 at 4:43 PM, Roberto Alonso CIPF ralo...@cipf.es 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,
On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion damion.doo...@bccdc.ca 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
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
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 p.j.a.c...@googlemail.com
wrote:
Thanks Dave, The good news is yes, the tests are running again on the Test
Tool Shed (although
Retitling thread,
On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com 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
On Fri, Jan 30, 2015 at 2:07 PM, Dannon Baker dannon.ba...@gmail.com 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=peterjcstatus=all
Internal Server Error
...
Trello issue logged,
https://trello.com/c
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
On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier d...@bx.psu.edu 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
On Tue, Jan 27, 2015 at 11:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier d...@bx.psu.edu 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
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
?
On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock p.j.a.c...@googlemail.com
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).
Perhaps
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 p.j.a.c...@googlemail.com
javascript:; wrote:
I think the symlink approach is best, see for example the Python
wrapper script I used here for samtools idxstats
, Jan 12, 2015 at 4:52 PM, Ryan G ngsbioinformat...@gmail.com 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 p.j.a.c...@googlemail.com
wrote:
Hi Ryan,
The problem isn't Galaxy stripping the extension, rather
On Tue, Jan 6, 2015 at 12:23 AM, Peter Cock p.j.a.c...@googlemail.com 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 you can only
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
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:
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