Hi David,
This is now fixed on tip:
https://bitbucket.org/galaxy/galaxy-central/changeset/83e024cee23d
Thanks,
K
On Sep 27, 2011, at 3:17 PM, David Hoover wrote:
> I apologize for responding to my own email, but I thought others might want
> to know.
>
> This turned out to be a Safari-depen
om:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Kanwei Li
> *Sent:* Wednesday, August 24, 2011 5:41 PM
>
> *To:* KOH Jia Yu Jayce
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] macs in galaxy
>
> ** **
>
Hi Shashi,
Does this only happen on your instance or does it happen on our public
instance as well?
Thanks,
K
On Fri, Sep 2, 2011 at 6:46 AM, shashi shekhar wrote:
> Hi All,
>
> i am not able to create workflow in my local instance of galaxy. it's
> displaying only loading picture on browser
Hi Shantanu,
Test usually tracks galaxy-central pretty closely, and we do update main
more often than galaxy-dist (you can see the version on main at the index
page). If nothing breaks on main for a while we do a galaxy-dist release so
we are generally confident that it will be stable.
Thanks,
K
p J
>
>
>
> -Original Message-
> *From:* Kanwei Li [mailto:kan...@gmail.com]
> *Sent:* Wednesday, August 24, 2011 11:28 PM
> *To:* KOH Jia Yu Jayce
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] macs in galaxy
>
>
>
> Hi Jayce,
>
>
>
>
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
%if param == True:
%else
%endif
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi wrote:
> Hi all,
>
> Is there a way to set the label of the output based on the input
> parameters? Perhaps by usi
in this email must be handled in accordance with the Information
> Privacy Act 2000 (Vic).
>
>
>
>
> On 25/08/2011, at 1:33 AM, Kanwei Li wrote:
>
> Hi Stephen,
>
> What platform are you running on?
>
> Thanks,
>
> K
>
> On Wed, Aug 24, 2011 at 3:53
The read_name has been implemented as well.
Thanks,
K
On Wed, Aug 24, 2011 at 1:15 PM, Kanwei Li wrote:
> Hi Shaun,
>
> Thanks for reporting this, I have just committed the fix. I will let you
> know if we add the read_name to the truncated output.
>
> -K
>
>
> On
Hi L-A,
I tried this on today's tip but could not reproduce the bug. I added your
param "" to a tool and the correct value was produced on the command line and in
the block as well. Re-running also gave the correct result.
Are you still seeing this problem?
Thanks,
K
2011/8/15 Louise-Amélie Sc
Hi Leandro,
I tested this on my instance and the example you gave did give me the
correct string: Human (hg18). Do you still have this problem? If so, can you
provide an example where it still behaves incorrectly?
Thanks,
K
On Thu, Jul 14, 2011 at 4:16 AM, Leandro Hermida wrote:
> Hi,
>
> Loo
Hi Shaun,
Thanks for reporting this, I have just committed the fix. I will let you
know if we add the read_name to the truncated output.
-K
On Tue, Aug 2, 2011 at 6:54 AM, SHAUN WEBB wrote:
>
> Hi, I've noticed a bug in sam2interval.py.
>
> There are a few indentation errors in the final lines
Hi Alex,
Sorry for the late reply. Can you elaborate more on your needs? Does the
Java app require filenames/params that can't be passed through the command
line?
Thanks,
K
On Mon, Jun 27, 2011 at 9:57 AM, Bossers, Alex wrote:
> Hello all,
>
> would it be possible to launch for instance a JAV
Hi Sarah,
Sorry for the late reply. The error is related to a bug we're currently
looking into. If you run it again, does it have this error consistently or
does it only happen once in a while?
Thanks,
K
On Thu, Jul 7, 2011 at 12:11 PM, Sarah Diehl wrote:
> Hi everybody,
>
> when I run the bu
Hi Joern,
Would it be easier to just chmod the directories to reflect the new user?
-K
On Wed, Aug 24, 2011 at 4:42 AM, Joern Toedling wrote:
> Hi all,
>
> we have our own Galaxy server running under Nginx. Recently we changed the
> 'user' of Nginx in the Nginx configuration file from 'galaxy'
Hi Stephen,
What platform are you running on?
Thanks,
K
On Wed, Aug 24, 2011 at 3:53 AM, Stephen Doyle wrote:
> Hello,
>
> I am in the process of installing a local instance, and I can't seem to be
> able to build the bx_python egg, even with scramble.py. Any ideas to get
> around this?
>
> Ch
Hi Jayce,
Are you running this on your local instance? It seems you are running MACS
1.4, which our wrapper does not support yet, but we are planning to add a
wrapper for 1.4 soon.
Thanks,
K
On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce
wrote:
> In running macs in galaxy, the following er
IE7/8 would require excanvas since it lacks official support. I'm guessing
at some point the excanvas hack wasn't applied to one of the canvases
created.
On Fri, Aug 19, 2011 at 7:45 AM, Hans-Rudolf Hotz wrote:
> Hi
>
> I am sorry to be a pain in the neck, but as part of our quarterly upgrade
>
Done
On Fri, Aug 12, 2011 at 5:36 AM, Peter Cock wrote:
> On Thu, Aug 11, 2011 at 4:11 PM, Jeremy Goecks
> wrote:
> >>> *The tool should work with general fasta files right now,
> >>> so the changes needed to support protein and other
> >>> fastas should be UI-based only.
> >>
> >> Right, while
The tool was committed in June :)
-K
On Fri, Aug 5, 2011 at 4:13 PM, Jennifer Jackson wrote:
> Hello Florent,
>
> I created a ticket to better track this request. I do not find that the
> changes were added yet (or that any decision about them was made), but if so
> and I just missed it, we can
Fixed on trunk, thanks for reporting!
K
On Thu, Jul 21, 2011 at 12:41 PM, Edward Kirton wrote:
>
> URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8
> Module paste.exceptions.errormiddleware:*143* in __call__
> Module paste.debug.prints:*98* in __call__
> Module paste.wsgilib:
Hi Nick,
Thank you! Although there was a tiny error in there with base_panels ;)
For the future, yes, please shoot an email to galaxy-dev and either
create a bitbucket issue with the patch, or have a link to the pull
request.
Thanks,
K
On Tue, Jul 19, 2011 at 11:25 AM, Nick Semenkovich wrote:
Hi Shaun,
It is included in galaxy... do you see the checkers.py file in
lib/galaxy/datatypes/checkers.py ?
-K
On Mon, Jul 18, 2011 at 11:31 AM, SHAUN WEBB wrote:
>
>
> Hi, I recently update to the latest dist release and I'm getting this error
> whenever I try to upload files
>
> Traceback (mo
Hi Hans,
I have created a ticket at BB:
https://bitbucket.org/galaxy/galaxy-central/issue/614/remove-the-select-all-and-unselect-all
Sorry for the late reply.
Thanks,
K
On Sat, May 7, 2011 at 9:02 AM, Hans-Rudolf Hotz wrote:
> Hi
>
> Is there a way to remove the "Select All" and "Unselect All
Hi Shantanu,
Thanks for the report. Is there any pattern to the files being marked
as empty? Certain filetype or histories?
-K
On Mon, Jul 11, 2011 at 3:07 PM, Shantanu Pavgi wrote:
>
> Hi,
>
> In our local galaxy install (currently revision 50e249442c5a) we are seeing
> few output datasets as
Hi Michal,
Can you elaborate on set on deleted items by default? It is always
"active" by default for me.
Thanks,
K
On Wed, Jul 6, 2011 at 3:23 AM, Michal Stuglik wrote:
>
> hi all,
>
> in galaxy-central:
>
> 1. default view in "Saved Histories" section is set on deleted items (
> Jeremy, I di
Hey Peter,
Right now the output is stored to a file, so we can do any processing
in python, or just keep the multi-line as it is. I agree
version_string should be version_cmd... didn't change it since working
on it at the Conference ;)
On Thu, Jul 7, 2011 at 6:27 AM, Peter Cock wrote:
> Hi all,
Is this from a recent changeset that you pulled?
On Wed, Jul 6, 2011 at 2:19 PM, Vipin TS wrote:
> Hi Galaxy team,
>
> I am experiencing a problem with visualizing my BAM files through Trackster
> at my Galaxy instance. Please find the attached image along with this mail.
> From the log file I am
Hi Ira,
This has been reported before as well, but should be fixed without having to
rescramble when we release our next dist-release soon.
Thanks,
K
On Wed, Jun 22, 2011 at 12:47 AM, Ira Cooke wrote:
> Hi,
>
> I recently downloaded galaxy and had some problems installing it on my
> machine (
What is the version for numpy in your eggs.ini?
On Wed, Jun 15, 2011 at 3:14 PM, Michael Steder wrote:
> Hi Nate,
>
> On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
>
> It should be working, this would have been a problem for a short time
> using galaxy-central, but should not have affected -di
ipts and wrappers.
> Regards,
> Florent
>
>
> On 27/05/11 18:49, Kanwei Li wrote:
>
> Has anyone on the list tried this patch? Feedback would be appreciated.
>
> Thanks,
>
> K
>
> On Fri, May 27, 2011 at 1:27 AM, Florent Angly wrote:
>
>> Can anyon
Fixed on trunk.
On Thu, Jun 9, 2011 at 10:26 AM, Nate Coraor wrote:
> Peter Cock wrote:
> >
> > It turned out to be quite quick to find what commit broke things:
> >
> > hg checkout 6074:a6868407f0e8
> > --> fails
> >
> > hg checkout 6073:d6b048e3483e
> > --> works
> >
> > Looks like 6074:a68684
Has anyone on the list tried this patch? Feedback would be appreciated.
Thanks,
K
On Fri, May 27, 2011 at 1:27 AM, Florent Angly wrote:
> Can anyone comment on my email please?
> Florent
>
>
>
> On 22/05/11 14:03, Florent Angly wrote:
>
> Let me know if you have any questions about this.
> Tha
Fixed on trunk by setting a default cntrller when there isn't one.
-K
On Thu, May 26, 2011 at 2:16 PM, Dave Walton wrote:
> Just removed user.pyc and restarted the server. Did not resolve the
> problem.
>
> Dave
>
>
>
> On 5/26/11 8:09 AM, "Greg Von Kuster" wrote:
>
> Hi Glen,
>
> I've neve
Hi Shashi,
You can add your own datatypes using the instructions here:
https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes
Thanks,
K
On Wed, May 25, 2011 at 1:05 PM, shashi shekhar wrote:
> Hi All,
>
> I have some problem with extension of file.some executables file will
> recog
Thank YOU for reporting them ;)
On Wed, May 25, 2011 at 11:33 AM, Leandro Hermida <
soft...@leandrohermida.com> wrote:
> Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE,
> for e.g. the workflow editor works now works and the history expand/collapse
> works! :)
>
> _
Sorry, it slipped by. Committed!
On Wed, May 25, 2011 at 12:48 PM, Peter Cock wrote:
> On Wed, May 18, 2011 at 6:40 PM, Peter Cock
> wrote:
> > Hi Kanwei,
> >
> > Could you merge this branch or transplant this fix please?
> >
> > https://bitbucket.org/peterjc/galaxy-central/changeset/3c0b903c86a
Hi Peter,
I think the tool shed would be appropriate for this...
-K
On Tue, May 17, 2011 at 6:23 AM, Peter Cock wrote:
> On Wed, May 4, 2011 at 9:59 AM, Peter Cock
> wrote:
> > Hi all,
> >
> > I mentioned just over a month ago that I had written a Galaxy tool
> > to do find Reciprocal Best Hit
Hi Assaf,
Nate has just committed a fix so this shouldn't be required now. Thanks for
the report!
K
On Thu, Apr 28, 2011 at 4:28 PM, Assaf Gordon wrote:
> I'll rephrase my question:
> Is "cython" going to be a standard requirement for Galaxy (and needs to be
> manually installed on our product
Thanks, fixed on trunk
On Sat, Apr 23, 2011 at 7:05 PM, Edward Kirton wrote:
> hello, after pulling the latest changes from galaxy-central, i get the
> following error:
>
> WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be
> fetched
>
> $ python scripts/fetch_eggs.py
> W
K
On Tue, Apr 19, 2011 at 11:22 AM, Peter Cock wrote:
> Hi Kanwei,
>
> I noticed that the BLAST+ output options for HTML are not working,
> a side effect of my recent refactoring. Could you transplant/merge this
> fix and test please:
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/e1e
Hi Liisa,
What does "hg tip" return?
K
On Mon, Apr 11, 2011 at 10:55 AM, Liisa Koski
wrote:
> Hi I just tried to update my local installation of Galaxy but accidentally
> hit Ctr-C when it asked me a question
>
> added 285 changesets with 649 changes to 354 files
> local changed static/script
Hi Louise,
Have you considered doing a SQL dump and import? Sounds easier to me
than writing a perl script ;)
-K
2011/4/8 Louise-Amélie Schmitt :
> Le vendredi 08 avril 2011 à 11:12 -0400, Sean Davis a écrit :
>> 2011/4/8 Louise-Amélie Schmitt :
>> > Hello everyone
>> >
>> > I just met a huge pr
Done the manual way
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of everything, thank you again!
>
> Daniel
>
>
> Am 04.04.2011 17:17, schrieb Kanwei Li:
>>
>> Hi Daniel,
>>
>> I have attached a patch that does this below. You can use it by
>> setting However the security is lacking as you
>> can see the strin
create new remote branches)
dhcp243253:galaxy-central kanwei$ hg merge blast25
abort: merging with a working directory ancestor has no effect
Importing the diffs gives merge error
On Mon, Apr 4, 2011 at 11:23 AM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 4:10 PM, Kanwei Li wrote:
>> I thi
Hi Daniel,
I have attached a patch that does this below. You can use it by
setting However the security is lacking as you
can see the string when you try to re-run the job and view source. Is
this sufficient for your purposes?
Thanks,
K
On Sat, Apr 2, 2011 at 11:01 AM, Daniel Schmidt wrote:
>
I think it's because the parent of those changesets were before your
merge, so the branches got messed up
On Mon, Apr 4, 2011 at 11:07 AM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 4:03 PM, Kanwei Li wrote:
>> I tried both ways, no dice (you can try yourself with a clean
>>
I tried both ways, no dice (you can try yourself with a clean
galaxy-central base)
On Mon, Apr 4, 2011 at 10:58 AM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 3:07 PM, Kanwei Li wrote:
>> Hi Peter,
>>
>> I think you need to merge your commits as I cannot seem to transp
Hi Peter,
I think you need to merge your commits as I cannot seem to transplant
or import the patches properly.
K
On Mon, Apr 4, 2011 at 9:46 AM, Peter Cock wrote:
> On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock wrote:
>> On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock
>> wrote:
>>> On Thu, Mar 31
Hi Peter,
I don't see your attempt to use default in the example given. A bit more detail?
-K
On Wed, Mar 30, 2011 at 12:32 PM, Peter Cock wrote:
> Hi all,
>
> I'm trying to write a new tool working with tabular data (specifically
> a Reciprocal Best Hits (RBH) tool using BLAST style tabular ou
Hi JJ,
This is fixed on trunk. If you don't want to upgrade yet, you can modify
eggs.ini to use the fixed eggs:
pysam = 0.4.1
[tags]
pysam = _kanwei_ae2bd50d9945
On Tue, Mar 22, 2011 at 4:13 PM, Jim Johnson wrote:
> We're getting a segfault from csamtool.so when the tracks controller is
> inv
Thanks for reporting this. I will improve the popups next week as they are
giving people lots of issues.
On Fri, Mar 18, 2011 at 12:05 PM, Peter Cock wrote:
> Hi all,
>
> I've been exploring how to use Galaxy's shared library functionality,
> and have noticed that once imported into a working his
Thanks for reporting, committed fix
On Fri, Mar 18, 2011 at 7:57 AM, Peter Cock wrote:
> Hi all,
>
> I just got a nasty recursion error when trying to run the functional
> tests for my TMHMM and
> SignalP wrappers - tools which produce tabular output.
>
> galaxy.jobs.runners.local: ERROR: Job wra
Hi Davide,
The summary_size is just the number of bins to aggregate the data over. It
can be greater than (end - start) because UCSC allows this, and so we allow
it too since we copy their method.
Kanwei
On Tue, Mar 8, 2011 at 2:23 AM, Davide Cittaro <
davide.citt...@ifom-ieo-campus.it> wrote:
Hi Peter,
The error when clicking tool menu links is now fixed on galaxy-central tip.
Thanks for reporting!
On Mon, Feb 21, 2011 at 4:48 AM, Peter wrote:
> > On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li wrote:
> >>
> >> All:
> >> I retested under IE7 and found t
Hi Peter,
The changes are on tip, which aren't in galaxy-dist or on main yet. I will
look into the other issues when I get access to my IE7 VM tomorrow.
Thanks!
K
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interfac
Hi Vasu,
Galaxy automatically sorts bam files, with samtools, on upload if they
aren't already sorted. Are you seeing instances where it's not the case?
Thanks,
Kanwei
On Fri, Feb 18, 2011 at 10:01 PM, vasu punj wrote:
> Can I sort (chr) bam file in Glaxay or I have to go back to samtools
> p
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li wrote:
> All:
>
> I retested under IE7 and found the bugs you were mentioning. This has all
> been fixed on trunk by using a newer local storage library. The only
All:
I retested under IE7 and found the bugs you were mentioning. This has all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On
This happens with a lot of the migration scripts... I think as long as
you have the new column (I just checked, mine does) it should be fine.
On Wed, Feb 2, 2011 at 9:11 AM, Peter Cock wrote:
> On Wed, Feb 2, 2011 at 1:27 PM, Peter Cock wrote:
>> Should I file a bug report?
>>
>> $ sh manage_db.
Committed
On Tue, Feb 1, 2011 at 10:27 AM, Peter wrote:
> Hi Kanewi,
>
> Sorry - make that three changesets on this branch to consider
> mering/transplanting:
> https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31
>
> Parameter handling,
> https://bitbucket.org/peterjc/galaxy-ce
I would think the get_fields way is more robust since you wouldn't run
into issues with special characters
On Tue, Jan 4, 2011 at 12:35 PM, Peter wrote:
> On Tue, Jan 4, 2011 at 2:26 AM, Daniel Blankenberg wrote:
>> Hi Peter (and -dev),
>>
>> Would something like ${param.fields.path} be preferre
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