Re: [galaxy-dev] prevent downloaded files with .txt added

[Kanwei Li]

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-dependent problem.  Lots of other people have 
> complained, but there doesn't seem to be any direct fix.
> 
> My quick solution was to make sure the downloaded file is gzipped.  This 
> kills two birds with one stone -- the download is smaller, and Safari doesn't 
> mess with the extension.
> 
> Now, does anyone know if it is possible to gzip a dataset from a history 
> within Galaxy prior to downloading?
> 
> David
> 
> On Sep 26, 2011, at 2:00 PM, David Hoover wrote:
> 
>> Does anyone know how to prevent the .txt suffix from being added to files 
>> downloaded from Galaxy?  For example, a fasta file is downloaded as 
>> xxx.fasta.txt, instead of xxx.fasta.
>> 
>> Wondering,
>> David Hoover
>> Helix Systems Staff
>> http://helix.nih.gov
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] macs in galaxy

[Kanwei Li]

I don't believe so, it looks like they generate a long config script (as you
can see in the xml file) and executes that.

K

On Thu, Sep 8, 2011 at 1:51 PM, Chorny, Ilya  wrote:

>  Is there a python script associated with the macs.xml file?
>
> ** **
>
> *From:* 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
>
> ** **
>
> You can use the MACS wrappers here (for 1.4):
> https://bitbucket.org/cistrome/cistrome-harvard/src/779d208c2cbd/tools/peakcalling/
> 
>
> ** **
>
> Until we officially add it to our distribution. 
>
> ** **
>
> Thanks,
>
> ** **
>
> K
>
> On Wed, Aug 24, 2011 at 8:32 PM, KOH Jia Yu Jayce 
> wrote:****
>
> Yes. Thank you for your help 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,
>
>  
>
> 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 error was found
>
>  
>
> ERROR:root:mfold format error! Your input is '32'. It should be like
> '10,30'
>
>  
>
> A format for mfold like 10,30 is expected… but the default value configured
> in xml remains as 32. will there be an updated version of this xml in
> future?
>
>  
>
> Also after altering the default display mfold value to 10,30, type integer
> in the param tag for mfold become erroneous. May I ask what is the correct
> type for input format 10,30?
>
>  
>
> Thanks alot
>
>  
>
>  
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
>  
>
> ** **
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Problems with load_workflow_editor

[Kanwei Li]

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 when i am clicking on edit option
> of workflow . how can we resolve such type of problem ? i am using old
> version version galaxy.
>
>
>
> 192.168.60.115, 145.139.1.156 - - [02/Sep/2011:16:13:50 +0600] "GET
> /workflow/get_datatypes?_=1314940546255 HTTP/1.1" 200 - "
> http://garu.ac.in/workflow/editor?id=df7a1f0c02a5b08e"; "Mozilla/5.0
> (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.17) Gecko/20110420
> Firefox/3.6.17"
> 192.168.60.115, 145.139.1.156 - - [02/Sep/2011:16:13:51 +0600] "GET
> /workflow/load_workflow?_=1314940546462&id=df7a1f0c02a5b08e&_=true HTTP/1.1"
> 200 - "http://garu.ac.in/workflow/editor?id=df7a1f0c02a5b08e"; "Mozilla/5.0
> (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.17) Gecko/20110420
> Firefox/3.6.17"
>
>
>
> Regards
> shashi shekhar
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] handling galaxy updates

[Kanwei Li]

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

On Fri, Sep 2, 2011 at 2:22 PM, Shantanu Pavgi  wrote:

>
> Hi,
>
> I am curious to know which revision of galaxy code gets deployed in the
> main ( http://main.g2.bx.psu.edu/ ) and test ( http://test.g2.bx.psu.edu/ ) 
> instances of galaxy. I was thinking active development repository
> galaxy-central code gets deployed in the test galaxy instance and stable
> galaxy-dist code gets deployed in the main galaxy instance.  However, it
> seems like main galaxy instance is updated more frequently than galaxy-dist
> repository. Should local galaxy instances keep up with PSU's main galaxy
> instance revisions or wait for stable code to be released in galaxy-dist
> repository? We have been keeping up with galaxy-dist repository and not the
> galaxy-central repository updates. Are  other sites following similar update
> model?
>
> --
> Thanks,
> Shantanu.
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] macs in galaxy

[Kanwei Li]

You can use the MACS wrappers here (for 1.4):
https://bitbucket.org/cistrome/cistrome-harvard/src/779d208c2cbd/tools/peakcalling/

Until we officially add it to our distribution.

Thanks,

K

On Wed, Aug 24, 2011 at 8:32 PM, KOH Jia Yu Jayce
wrote:

>  Yes. Thank you for your help 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,
>
>
>
> 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 error was found
>
>
>
> ERROR:root:mfold format error! Your input is '32'. It should be like
> '10,30'
>
>
>
> A format for mfold like 10,30 is expected… but the default value configured
> in xml remains as 32. will there be an updated version of this xml in
> future?
>
>
>
> Also after altering the default display mfold value to 10,30, type integer
> in the param tag for mfold become erroneous. May I ask what is the correct
> type for input format 10,30?
>
>
>
> Thanks alot
>
>
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Setting the output label based on input parameters?

[Kanwei Li]

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 using the  tag?  Basically, I want the
> output label to be different if the user sets a particular parameter to be
> true.
>
> - Nik.
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Installing local instance hiccup

[Kanwei Li]

Ah, unfortunately we don't have a machine running Lion that can build the
bundled eggs. Any chance you could change it to 2.6? "man python" in the
command line should give instructions.

For 10.6, the command is "defaults write com.apple.versioner.python Version
2.6"

On Wed, Aug 24, 2011 at 6:20 PM, Stephen Doyle wrote:

> Hi Kanwei,
>
> That would certainly help. Its a new MacBook Pro running OSX 10.7.1 and
> Lion.
>
> Cheers,
> Steve
>
>
>
>
>
> -
> Dr Stephen R. Doyle
> Postdoctoral Researcher
> Genetics Department | La Trobe University | Bundoora 3086
> Australia
> T: +61 3 9479 3087 |  F: +61 3 9479 2480 | E: s.do...@latrobe.edu.au | W:
> http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm
>
> *La Trobe University - ranked top in Victoria for student satisfaction
> (Sweeney Uni Student Report, 2009)
> *
> CRICOS Provider 00115M
>
> J Please kindly consider your environment before printing this e-mail
>
> Warning to recipients:
> This email and any attachments are confidential and subject to copyright.
> If you are not the intended recipient any use, disclosure or copying is
> unauthorised. If you have received this email in error please advise us
> immediately by reply email and delete all copies. It is your responsibility
> to examine this email and any attachments for viruses. Any personal
> information 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 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?
>>
>> Cheers,
>> Steve
>>
>>
>>
>>
>>
>> -
>> Dr Stephen R. Doyle
>> Postdoctoral Researcher
>> Genetics Department | La Trobe University | Bundoora 3086
>> Australia
>>  T: +61 3 9479 3087 |  F: +61 3 9479 2480 | E: s.do...@latrobe.edu.au |
>> W: http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm
>>
>> *La Trobe University - ranked top in Victoria for student satisfaction
>> (Sweeney Uni Student Report, 2009)
>> *
>> CRICOS Provider 00115M
>>
>> J Please kindly consider your environment before printing this e-mail
>>
>> Warning to recipients:
>> This email and any attachments are confidential and subject to copyright.
>> If you are not the intended recipient any use, disclosure or copying is
>> unauthorised. If you have received this email in error please advise us
>> immediately by reply email and delete all copies. It is your responsibility
>> to examine this email and any attachments for viruses. Any personal
>> information in this email must be handled in accordance with the Information
>> Privacy Act 2000 (Vic).
>>
>>
>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>>
>
>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Sam2interval.py bug

[Kanwei Li]

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 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 of code. I think
>> there should be an indent after:
>>
>>if not ref_name == '*':
>>
>> And this whole if statement should be included in the for loop above.
>>
>>
>> Also, would you be able to add read_name to the truncated output (when not
>> printing all fields). This makes downstream analysis a lot easier, e.g.
>> looking at reads that map multiple times.
>>
>> Thanks
>> Shaun Webb
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>>
>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] checkboxes bug fix

[Kanwei Li]

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 Schmitt 

> Hello,
>
> Sorry for being late, again, but please find the tool attached.
>
> Here is my last pull: 5743:720455407d1c
>
> Stuff changed in the file but in the end I had to make the same
> modification again (change true to false) since it didn't work anymore.
>
> Best,
> L-A
>
>
>
> Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit :
>
>  Hi, and sorry for the late reply
>>
>> Here is the last pull: 5355:50e249442c5a
>>
>> I'll try to be as concise as I can but I can send you the whole file if
>> you need it. It's not completely done yet though.
>>
>> This is a tool that produces a HTML file containing the results of various
>> quality assessment programs. To trigger or block the execution of a specific
>> program, I use checkboxes in the form, like this:
>> 
>>
>> Then, I use the  tags to define a shell script
>> that will be modified with cheetah tests on the checkboxes.
>>
>> Then the final script is sent to another shell script  that will check its
>> existence and launch it:
>> all_QA.sh $script 
>>
>> As you can see, the checkboxes are checked by default. But before the
>> change I mentioned is my last email, un-checking them didn't have any effect
>> whatsoever. The following test, for instance, was always true:
>> #if $SQA.value == True
>>
>> Moreover, even if I un-checked the checkboxes and ran the tool, then
>> clicked the re-run button in the result in my history, all of them were
>> checked in the form that appears, as if I never un-checked them.
>>
>> Now, the state of the checkboxes is respected and I can properly choose
>> what to run in my tool.
>>
>> Hope that helps.
>> L-A
>>
>>
>> Le 08/06/2011 20:54, Jennifer Jackson a écrit :
>>
>>> Hi L-A,
>>>
>>> Could you describe a use case (which tool/from, what options/input)? If
>>> you know the last pull # for your local install, that would also be helpful
>>> for us to know.
>>>
>>> Best,
>>>
>>> Jen
>>> Galaxy team
>>>
>>> On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote:
>>>
 Hi,

 Since I haven't updated Galaxy for a while now I don't know if it was
 actually fixed but I had issues with my default-selected checkboxes:

 When I deselected them, the value sent in the query remained as if they
 were still selected. Even when I re-ran the job, all the checkboxes were
 selected as if I never deselected them.

 Therefore, in lib/galaxy/web/form_builder.py

 I changed:
 105 return '>>> value="true"%s%s>' \

 for:
 105 return '>>> value="true"%s%s>' \

 And it works fine now :)

 Cheers,
 L-A
 __**_
 Please keep all replies on the list by using "reply all"
 in your mail client. To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

>>>
>>>
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] value_label tool input param attribute doesn't work as documented

[Kanwei Li]

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,
>
> Looking at the example on the Tool Config Syntax wiki page:
> Example
>
> Assume that the tool includes an input parameter named "database" which is
> a select list ( e.g., assume the following inputs ):
>  Toggle line 
> numbers
>
>1 
> 
>  
>2 
> 
>  
>3 
> 
>  
>4 
> 
>  *Human (hg18)*
>5 
> 
>  Fly (dm3)
>6 
> 
>  
>7 
> 
>  
>
> Assume that the user selects the first option in the $database select
> list. Then the following will ensure that the tool produces a tabular data
> set whose associated history item has the label "Blat on *Human (hg18)*".
> Toggle line 
> numbers
>
>1 
> 
>  
>2 
> 
>  
>3 
> 
>  
>
> It shows that .value_label attribute should produce the string in between
> the  tags, not the actual value.
>
> Why does this not work? When I use it it produces the value, or am I doing
> something wrong?
>
> regards,
> Leandro
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Sam2interval.py bug

[Kanwei Li]

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 of code. I think
> there should be an indent after:
>
>if not ref_name == '*':
>
> And this whole if statement should be included in the for loop above.
>
>
> Also, would you be able to add read_name to the truncated output (when not
> printing all fields). This makes downstream analysis a lot easier, e.g.
> looking at reads that map multiple times.
>
> Thanks
> Shaun Webb
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Launching a JAVA or external app

[Kanwei Li]

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 JAVA app with preloaded
> parameters and files from galaxy that needs interaction/display?
> For instance a gui based annotation editor? It necessarily doesn't have to
> support saving of files back to galaxy. Sort of end stage.
> Any help or pointers appreciated.
> thanks
> Alex
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Error when using build_profile_indexes.py on hg19

[Kanwei Li]

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 build_profile_indexes.py script in the
> scripts/tools/annotation_**profiler/ directory on hg19 (downloaded
> yesterday from UCSC), I get the following error:
>
> Created table dir (profiled_annotations/hg19/**
> wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal).
> ['fileName']
> Table wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal
> (/galaxy/galaxy_data/ucsc_**data/hg19/**wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal.sql)
> does not appear to have a chromosome, a start, or a stop.
> Removing empty table (**wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal)
> directory (profiled_annotations/hg19/**wgEncodeOpenChromFaireGlioblaB**
> aseOverlapSignal).
> Created table dir (profiled_annotations/hg19/**
> wgEncodeCshlShortRnaSeqK562Chr**omatinShortTransfrags).
> ['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand',
> 'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount',
> 'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount',
> 'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount',
> 'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength',
> 'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY']
> Traceback (most recent call last):
>  File "/galaxy/galaxy_backup/galaxy-**dist/scripts/tools/annotation_**
> profiler/build_profile_**indexes.py", line 338, in 
>if __name__ == "__main__": __main__()
>  File "/galaxy/galaxy_backup/galaxy-**dist/scripts/tools/annotation_**
> profiler/build_profile_**indexes.py", line 310, in __main__
>bitset_dict[ chrom ].set_range(  start, end - start  )
>  File "bitset.pyx", line 128, in bx.bitset.BitSet.set_range
> (lib/bx/bitset.c:1130)
>  File "bitset.pyx", line 93, in bx.bitset.b_check_range_count
> (lib/bx/bitset.c:656)
> IndexError: End 16573 is larger than the size of this BitSet (16571).
>
>
> Everything worked fine with mm9 and dm3.
>
> Since the script wasn't changed in the last year, I suspect it has to do
> with the UCSC data.
>
> We don't really use hg19, so I'm fine with just leaving it out for now, but
> I wanted to report the error anyway.
>
> Best regards,
> Sarah
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Issue with file permissions of uploaded files

[Kanwei Li]

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' to a more
> general 'www' since we plan to use Nginx for other purposes as well.
>
> Now the "Get data -> Upload file" does not work any longer because of file
> permissions. Files are uploaded correctly to a directory
> /local/data/galaxy_tmp/upload_**store/
> but then are owned by the 'www' user and read-writeable by this other only.
> Thus, the Galaxy user 'galaxy' cannot open them, cannot determine the file
> type and the whole "Upload file" process fails.
>
> How can I set the file permissions of uploaded files? Do I need to enter a
> matching 'umask' in some Galaxy configuration or in some Nginx configuration
> file. Any links to where to set such a umask would be greatly appreciated.
>
> Thanks,
> Joern
>
> --
> Joern Toedling, PhD
> Core Facility Bioinformatics
> Institute of Molecular Biology gGmbH (IMB)
> http://www.imb-mainz.de
> Tel.: +49 6131 39 21511
>
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Installing local instance hiccup

[Kanwei Li]

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?
>
> Cheers,
> Steve
>
>
>
>
>
> -
> Dr Stephen R. Doyle
> Postdoctoral Researcher
> Genetics Department | La Trobe University | Bundoora 3086
> Australia
> T: +61 3 9479 3087 |  F: +61 3 9479 2480 | E: s.do...@latrobe.edu.au | W:
> http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm
>
> *La Trobe University - ranked top in Victoria for student satisfaction
> (Sweeney Uni Student Report, 2009)
> *
> CRICOS Provider 00115M
>
> J Please kindly consider your environment before printing this e-mail
>
> Warning to recipients:
> This email and any attachments are confidential and subject to copyright.
> If you are not the intended recipient any use, disclosure or copying is
> unauthorised. If you have received this email in error please advise us
> immediately by reply email and delete all copies. It is your responsibility
> to examine this email and any attachments for viruses. Any personal
> information in this email must be handled in accordance with the Information
> Privacy Act 2000 (Vic).
>
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] macs in galaxy

[Kanwei Li]

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 error was found
>
>
>
> ERROR:root:mfold format error! Your input is '32'. It should be like
> '10,30'
>
>
>
> A format for mfold like 10,30 is expected… but the default value configured
> in xml remains as 32. will there be an updated version of this xml in
> future?
>
>
>
> Also after altering the default display mfold value to 10,30, type integer
> in the param tag for mfold become erroneous. May I ask what is the correct
> type for input format 10,30?
>
>
>
> Thanks alot
>
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] trackster problem with IE8 and IE7 when using "June 23, 2011" release

[Kanwei Li]

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
> procedure, I am stumbling across the next problem:
>
> Can anybody confirm, that the visualization does not work with the
> "June 23, 2011" release (changeset: 5743:720455407d1c) when using  IE8 or
> IE7 on windows XP?
>
> (it works with chrome and firefox6 on windows XP, and no problems with mac
> and linux)
>
>
> And like the previous problems, is there a quick fix available?
>
>
> Thank you very much for your help
> Regards, Hans
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Extracting regions of sequences given table of co-ords

[Kanwei Li]

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 of course preserving the (now misleading) tool
> >> ID of  "Extract genomic DNA 1" and filename of
> >> extract/extract_genomic_dna.xml for backwards
> >> compatibility.
> >
> > Only the tool ID is required for backwards compatibility; the filename
> can be changed.
>
> OK.
>
> First, some minor house keeping - if you can clarify the text
> for how a user should go from a tabular file to an interval or
> GFF file, that would be good:
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/d41ee8c41532
>
> Could you transplant/merge that please? Its the only commit
> so far on my new branch:
>
> https://bitbucket.org/peterjc/galaxy-central/src/extract_region
>
> Regards,
>
> Peter
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Request for pulling the updated FASTQ (de-)interlacer tool

[Kanwei Li]

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 update/close the bitbucket ticket.
> https://bitbucket.org/galaxy/**galaxy-central/issue/636
>
> Thanks for contributing to Galaxy!
>
> Jen
> Galaxy team
>
>
> On 5/17/11 12:47 AM, Florent Angly wrote:
>
>> Dear Galaxy team,
>> Please consider pulling these changes I made to the
>> interlacer/de-interlacer tools into the main Galaxy repository:
>> https://bitbucket.org/fangly/**galaxy-central/changeset/**7f7ec8f05d36
>> While the tools were handling mate pairs fine, I now added the ability
>> to also keep single reads (reads that miss their mate) in a separate
>> file. The functional tests were updated and pass.
>> Thanks,
>> Florent
>>
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>>
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/**Support 
>
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] workflows are broken in current galaxy-central version

[Kanwei Li]

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:*539* in intercept_output
> Module paste.recursive:*80* in __call__
> Module paste.httpexceptions:*632* in __call__
> Module galaxy.web.framework.base:*145* in __call__
> >>   body
>  *=* method*(* trans*,* kwargs *)*
> Module galaxy.web.framework:*84* in decorator
> >>   *
> return* func*(* self*,* trans*,* ***args*,* kwargs *)*
> Module galaxy.web.controllers.workflow:*686* in editor
> >>   *
> return* trans*.*fill_template*(* "workflow/editor.mako"*,* stored*=*stored
> *,* annotation*=*self*.*get_item_annotation_str*(* trans*.*sa_session*,*
> trans*.*user*,* stored *)* *)*
> Module galaxy.web.framework:*661* in fill_template
> >>   *
> return* self*.*fill_template_mako*(* filename*,* kwargs *)*
> Module galaxy.web.framework:*672* in fill_template_mako
> >>   *
> return* template*.*render*(* data *)*
> Module mako.template:*296* in render
> >>   *
> return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)*
> Module mako.runtime:*660* in _render
> >>   
> _kwargs_for_callable*(*callable_*,* data*)**)*
> Module mako.runtime:*692* in _render_context
> >>   
> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)
> *
> Module mako.runtime:*718* in _exec_template
> >>   
> callable_*(*context*,* ***args*,* kwargs*)*
> Module _base_panels_mako:*87* in render_body
> >>   
> __M_writer*(*unicode*(*self*.*overlay*(*visible*=*self*.*overlay_visible*)
> **)**)*
> *TypeError: render_overlay() got an unexpected keyword argument 'visible'*
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Pull request for Galaxy

[Kanwei Li]

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 --
>
> I just submitted a tiny first pull request for some minor Galaxy
> changes (to correct wiki links):
> https://bitbucket.org/galaxy/galaxy-central/pull-request/2/update-galaxy-wiki-links
>
> (Not sure if I should e-mail the dev list about these or what. How do
> these get approved?)
>
>
> Thanks!
> Nick
>
> --
> Nick Semenkovich
> 314.374.4434
>
> Medical Scientist Training Program
> School of Medicine
> Washington University in St. Louis
> http://web.mit.edu/semenko/
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] checkers

[Kanwei Li]

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 (most recent call last):
>  File "/storage/home/galaxy/test/galaxy-dist/tools/data_source/upload.py",
> line 11, in
>    from galaxy.datatypes.checkers import *
> ImportError: No module named checkers
>
> Should this module be provide with Galaxy or do I have to download it from
> somewhere?
>
> Thanks
> Shaun
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] removing "Select All" / "Unselect All" buttons from a set of check boxes

[Kanwei Li]

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" buttons from a
> set of check boxes?  - crated with:
>
>        display="checkboxes" multiple="true"
>       dynamic_options="ds_samplesFromServer()"/>
>
>
>
> I have a very long list, and I don't want to encourage people to tick all
> boxes.
>
>
> Thank you very much for your help, Hans
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] empty status for non-empty datasets

[Kanwei Li]

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 'empty' in the galaxy web interface. The actual file 
> size on the filesystem is ~ 4GB. These 'empty' files can be downloaded by 
> clicking on download/view icons, however they can't be imported in other 
> workflows. I looked into the database and figured out that file_size column 
> value for corresponding dataset id is zero. I am guessing that's why it is 
> being shown as empty in the web interface. Any suggestions on how to resolve 
> this will be helpful.
>
> --
> Thanks,
> Shantanu.
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Saved Histories - default view on deleted histories (bug)

[Kanwei Li]

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 did double check this morning on fresh instance :))
> 2. in advanced search option: one of the filter switch is deleted and does
> the same job as active switch
>
> 3. Sugestion:
>
> Saved Histories->Advanced Search
>
> sharing:     private | shared | accessible | published | all
> deleted:     active | deleted | all
>
> maybe it is better to change it to:
>
> sharing:     private | shared | accessible | published | all
> status:     active | deleted | all
>
> I think "deleted" is not clear..
>
> all the best,
> michal
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] New tag in tool XML

[Kanwei Li]

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,
>
> This new feature looks very exciting for tracking reproducibility -
> now in theory both the tool wrapper version (explicit in the XML)
> and any underlying tool version will both be recorded:
>
> https://bitbucket.org/galaxy/galaxy-central/changeset/84b20f29dfdf
>
> I have updated the NCBI BLAST+ wrappers to use the new
> feature, please merge/transplant this branch/commit:
>
> https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_07_07
> https://bitbucket.org/peterjc/galaxy-central/changeset/11f425f4e137
>
> I hope the new tool version string will get its own field in the
> database soon (and be viewable via the web interface). Note
> that string may well be multi-line, e.g.
>
> $ blastp -version
> blastp: 2.2.25+
> Package: blast 2.2.25, build Apr  6 2011 13:59:28
>
> Unless that is you go for more fragile solutions like these to
> ensure a single line:
>
> $ samtools 2>&1 | grep -i "^Version"
> Version: 0.1.16 (r963:234)
>
> $ bwa 2>&1 | grep -i "^Version"
> Version: 0.5.9-r16
>
> Thanks,
>
> Peter
>
> P.S. I would say the name  is a bit confusing,
> I'd have picked  or  instead.
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] BAM display at Trackster

[Kanwei Li]

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 not seeing any clues about the error message which is
> displayed on my browser page (A dependency (bai) was in an error state.)
>
> I updated my instance recently, It will be great if you can help me on the
> same.
>
> Thanks in advance,
> Vipin
> Friedrich Miescher Laboratory
> of the Max Planck Society
> Tuebingen
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Installation problems on osx

[Kanwei Li]

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 (running Mac OSX 10.6.7 ).  I've found a workaround to my problem,
> but I thought I should post here in case it is useful.
>
> I obtained the standard galaxy distribution using
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
>
> I then tried running sh run.sh but got;
>
> Traceback (most recent call last):
>  File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/buildapp.py",
> line 81, in app_factory
>from galaxy.app import UniverseApplication
>  File "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/app.py", line 11, in
> 
>from galaxy.tools.imp_exp import load_history_imp_exp_tools
>  File
> "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py",
> line 6, in 
>from galaxy.web.base.controller import UsesHistory
>  File
> "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/web/base/controller.py",
> line 12, in 
>from galaxy.visualization.tracks.data_providers import get_data_provider
>  File
> "/Users/iracooke/Sources/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py",
> line 16, in 
>from bx.arrays.array_tree import FileArrayTreeDict
>  File "numpy.pxd", line 119, in init bx.arrays.array_tree
> (lib/bx/arrays/array_tree.c:11323)
> ValueError: numpy.dtype does not appear to be the correct type object
>
>
> I googled this error and found a post suggesting that I try virtualenv ...
> I tried that but it made no difference.
>
> Python --version returns
> 2.6.1
>
> After some digging I tried rescrambling the numpy and then the bx_python
> egg.  After rescrambling the latter sh run.sh worked.
>
> Anyway I'm not sure if other mac users have had similar problems.  In my
> case I'm pretty sure I had installed things with easy_install in the past
> ...but I assume using virtualenv would have solved that problem.
>
> Ira
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] [galaxy-user] Error running latest Galaxy Distribution: numpy.dtype exception

[Kanwei Li]

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 -dist.  Could you
> send the output of:
>
>  python ./scripts/get_platforms.py
>  python -V
>
>
> $ python ./scripts/get_platforms.py
> macosx-10.6-universal-ucs2
> $ python -V
> Python 2.6.1
>
>
> Should I be running galaxy-central instead?
>
>
> No, galaxy-dist is fine (and should be less prone to issues due to
> cloning/updating at the wrong moment).
>
> Thanks,
> --nate
>
>
> Just in case it helps:
>
> I'm currently running tip of galaxy-dist:
>
> hg tip
> changeset:   5585:8c11dd28a3cf
> tag: tip
> user:Nate Coraor 
> date:Thu May 19 10:07:53 2011 -0400
> summary: Add Picard and fastqc tools to Main
>
> My prior version which is still working for me is:
>
> changeset: 5355:50e249442c5a user: Daniel Blankenberg 
> date: Thu Apr 07 08:39:07 2011 -0400 summary: Additional fix for typo
> propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
>
> ~Mike
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool

[Kanwei Li]

Committed on trunk.

On Thu, Jun 2, 2011 at 2:25 AM, Florent Angly wrote:

>  Hi Kanwei,
> I think we'll get more feedback once it when it is added to Galaxy. I have
> run small tests (included in the functional tests) and real large datasets
> and have had no issues with the scripts 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 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.
>> Thanks,
>> Florent
>>
>>  Original Message   Subject: Request for pulling the
>> updated FASTQ (de-)interlacer tool  Date: Tue, 17 May 2011 17:47:13 +1000  
>> From:
>> Florent AnglyTo:
>> galaxy-dev@lists.bx.psu.edu 
>> 
>>
>> Dear Galaxy team,
>> Please consider pulling these changes I made to the
>> interlacer/de-interlacer tools into the main Galaxy 
>> repository:https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36
>> While the tools were handling mate pairs fine, I now added the ability
>> to also keep single reads (reads that miss their mate) in a separate
>> file. The functional tests were updated and pass.
>> Thanks,
>> Florent
>>
>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>  http://lists.bx.psu.edu/
>>
>
>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] ValueError: numpy.dtype does not appear to be the correct type object

[Kanwei Li]

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:a6868407f0e8 is the cause then, which makes sense
> > since it jumps from NumPy 1.3.0 to NumPy 1.6.0:-
> >
> > changeset:   6074:a6868407f0e8
> > user:Nate Coraor 
> > date:Wed Jun 08 23:50:07 2011 -0400
> > summary: Testing Python 2.7.
> >
> > https://bitbucket.org/galaxy/galaxy-central/changeset/a6868407f0e8
> >
> > Probably some of the eggs need to be updated.
>
> bx_python needs to be rebuilt using the new version of the numpy egg.  I
> am doing this now and they should be up shortly.
>
> --nate
>
> >
> > Peter
> >
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool

[Kanwei Li]

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.
> Thanks,
> Florent
>
>  Original Message   Subject: Request for pulling the
> updated FASTQ (de-)interlacer tool  Date: Tue, 17 May 2011 17:47:13 +1000  
> From:
> Florent AnglyTo:
> galaxy-dev@lists.bx.psu.edu 
> 
>
> Dear Galaxy team,
> Please consider pulling these changes I made to the
> interlacer/de-interlacer tools into the main Galaxy 
> repository:https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36
> While the tools were handling mate pairs fine, I now added the ability
> to also keep single reads (reads that miss their mate) in a separate
> file. The functional tests were updated and pass.
> Thanks,
> Florent
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

[Kanwei Li]

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 never seen this before, but perhaps your user controller is using an
> old version ( I'm just grasping here, because this is pretty obscure
> behavior ).  Try deleting the following file - make sure it is the .pyc
> file.
>
> ~/lib/galaxy/web/controllers/user.pyc
>
> The user controller contains the code that generates the you may create one
>   link, but the current versions of
> this controller is using the new method signature as well, so the only thing
> I can think of is that your compiled version ( user.pyc ) is old.
>
>
> Let us know if this doesn't resolve the issue.
>
> Thanks!
>
> On May 26, 2011, at 7:39 AM, Glen Beane wrote:
>
>  I just checked,
>
> Using the User->Register menu works,  however we require our users to log
> in so when they go to galaxy.jax.org   they are
> redirected to a login page if they are not already logged in.  That page has
> the text "This installation of Galaxy has been configured such that only
> users who are logged in may use it. If you don't already have an account,
> you may create one  ."  , and "you may
> create one" links to http://galaxy.jax.org/user/create.  clicking on the
> link results in the error.
>
>
> -glen
>
>
> On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote:
>
>  Hello Dave,
>
> Can you clarify how your users are accessing the following URL
>
>   http://galaxy.jax.org/user/create
>
>
> I originally assumed they were using the Galaxy UI to register by clicking
> the "Register" link on the "User" popup menu.  However, perhaps they are
> just pointing their browser to the URL.  Is this the case?  If so, why are
> you not clicking on the menu link?
>
> If it is the case that your users are entering the address in their
> browsers rather than using the normal Galaxy UI, then the address should
> include an additional request param as is shown here:
>
>   http://galaxy.jax.org/user/create?cntrller=user
>
>
> Greg
>
>
> ~/
> On May 25, 2011, at 1:46 PM, Dave Walton wrote:
>
>  Greg.
>
> We do not use the "template_cache_path" in our config.  I deleted all the
> files in ~/database/compiled_templates and restarted my server.  I still
> get
> the error (even with a shift reload of my browser).  I've tried it (on the
> Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71
>
> We run two totally separate instances of Galaxy, on different virtual
> machines.  One for testing, development of tools and deploying new versions
> of galaxy, and one for production, where our scientists do their analysis.
> Each of these servers run 4 instances of the "galaxy process".  3 Web
> applications and 1 job runner.
>
> We get the error on both servers, but I'm doing all of this troubleshooting
> on our development server.
>
> This behavior is occuring for any user who tries to create a new galaxy
> account (so the original user who reported the problem, and myself as I
> test
> it.  I can ask others to try if you think that will help).
>
> I mentioned the browsers I've tried it with above.  I've not tried it from
> a
> windows box, but can, again, if you think that will help.
>
> We are running whatever version of galaxy-dist was available about a week
> and a half ago, which is when Glen did the upgrade.
>
> Thanks,
>
> Dave
>
>
> On 5/24/11 11:29 PM, "Greg Von Kuster"  wrote:
>
>  Hi Dave,
>
> If you do not have a template_cache_path config setting in
> universe_wsgi.ini,
> then your cached templates are stored in the default directory of
> ~/database/compiled_templates.
>
> Deleting your cached templates in ~/database/compiled_templates should have
> corrected the problem, assuming there are no other issues within your
> Galaxy
> environment, so let's begin down the path of determining the cause.
>
> You mention your "development server" in your response.  Are you running
> only
> 1 Galaxy instance, or more than 1?
>
> Is the behavior occurring for all of your users or just a few?  Does it
> occur
> with different browsers, or is it related to a certain browser brand?
>
> What version of Galaxy are your running?
>
> Thanks Dave,
>
> Greg Von Kuster
>
> On May 24, 2011, at 6:06 PM, Dave Walton wrote:
>
>  Greg,
>
> We've tried just reloading the browser and that didn't do anything.
>
> As for deleting the cached templates, on our development server I tried
> deleting everything under the database/compiled_templates directory (I even
> restarted my server) and it appeared to have no affect.  We still get the
> error message.  Maybe I misunderstood you.
>
> The only cache related variable in my universe_wsgi files is
> "static_cache_time = 360".
>
> Thanks,
>
> Dave
>
>
> On 

Re: [galaxy-dev] Problem with file's extension

[Kanwei Li]

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
> recognize the only the specific extension like autodock . it takes one
>  input file ( extension with  ".dpf" ) and one  outpt file (extension with
> ".dlg"). how can we resolve such type of problem .
>
>
> Regards
>
> Shashi shekhar
>
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] new galaxy-dist fixes multiple IE UI bugs

[Kanwei Li]

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! :)
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Galaxy BLAST XML to tabular fix

[Kanwei Li]

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/3c0b903c86a9
> >
> > https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_05_18
> >
> > New branch, blast_2011_05_18
> >
> > There is no change to the logic, just to the assert statement where
> > the sanity test didn't consider doubly masked sequences.
> >
> > Should I also update the XML wrapper's version number as well?
> >
> > Thanks,
> >
> > Peter
>
> Hi Kanwei,
>
> Did this email reach you? Let me know if you want a new unit
> test to go with it and/or to bump the tool's version number.
>
> Regards,
>
> Peter
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Reciprocal Best Hits (RBH) from BLAST tabular output

[Kanwei Li]

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 Hits (RBH) from BLAST tabular output
> > or similar (e.g. Bill Pearson's FASTA tabular output).
> >
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004825.html
> > http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004829.html
> >
> > The only problem I had was setting default columns, which I
> > consider to be a minor bug in Galaxy:
> >
> > https://bitbucket.org/galaxy/galaxy-central/issue/507
> >
> > Regardless of this small usability issue, would the Galaxy team
> > like to add this tool to the main distribution (to sit along with my
> > BLAST+ wrappers), or should I submit it to the tool shed?
> >
> > If you want to merge it, the following change set should suffice:
> > https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30
> >
> > I made a subsequent change set to test giving column defaults
> > as value="c2" rather than value="c2" which makes no difference,
> > but if this is how default column values are meant to be given,
> > take this change too:
> > https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30
>
> A third commit fixes a typo in the help:
> https://bitbucket.org/peterjc/galaxy-central/changeset/2be6c0bc76ea
>
> Would the Galaxy team like to merge this tool into the trunk
> (and if so, do you have any suggestions for improvements or
> changes), or should I put it up on the Galaxy Tool Shed instead?
>
> Thanks,
>
> Peter
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] problem running latest "galaxy-central"

[Kanwei Li]

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 production servers), or is this just a temporary
> thing, or is it going to be an automatic egg thing ?
>
> WATSON Mick wrote, On 04/28/2011 04:11 PM:
> > Looks like it :)
> >
> > http://cython.org/#download
> > 
> > From: galaxy-dev-boun...@lists.bx.psu.edu [
> galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Assaf Gordon [
> gor...@cshl.edu]
> > Sent: 28 April 2011 20:52
> > To: galaxy-...@bx.psu.edu
> > Subject: [galaxy-dev] problem running latest "galaxy-central"
> >
> > Question:
> >
> > The recent galaxy-central revision ( 2b057869b72f ) doesn't work on my
> computer, saying "DistributionNotFound: cython>=0.12.1".
> >
> > Example:
> > $ hg clone 
> > http://bitbucket.org/galaxy/galaxy-central/galaxy_hidden_dataset_test
> > $ cd galaxy_hidden_dataset_test
> > $ hg id
> > 2b057869b72f tip
> > $ sh run.sh
> > ...
> > ...
> > ...
> > Traceback (most recent call last):
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/buildapp.py",
> line 81, in app_factory
> > from galaxy.app import UniverseApplication
> >   File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/app.py",
> line 11, in 
> > from galaxy.tools.imp_exp import load_history_imp_exp_tools
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/tools/imp_exp/__init__.py",
> line 6, in 
> > from galaxy.web.base.controller import UsesHistory
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/base/controller.py",
> line 12, in 
> > from galaxy.visualization.tracks.data_providers import
> get_data_provider
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/visualization/tracks/data_providers.py",
> line 11, in 
> > pkg_resources.require( "pysam" )
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 404, in require
> > return c[req.project_name].require()
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 237, in require
> > dists = self.resolve()
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 195, in resolve
> > return self.version_conflict( e.args[0], e.args[1] )
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py",
> line 226, in version_conflict
> > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
> env, egg.fetch )
> >   File
> "/home/gordon/temp/galaxy_hidden_dataset_test/lib/pkg_resources.py", line
> 565, in resolve
> > raise DistributionNotFound(req)  # XXX put more info here
> > DistributionNotFound: cython>=0.12.1
> >
> > =
> >
> > I'm running debian/stable, with Python 2.6.6 (r266:84292, Dec 26 2010,
> 22:31:48)
> >
> > Do I need to install something (cython) ?
> >
> > -gordon
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >   http://lists.bx.psu.edu/
> >
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] MarkupSafe egg cannot be fetched

[Kanwei Li]

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
> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] BLAST+ HTML output broken

[Kanwei Li]

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/e1e6f92e07bf
> https://bitbucket.org/peterjc/galaxy-central/changeset/c60551f7d13c
>
> These are the only commits on this new branch from the default:
>
> https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_04_19
>
> Thanks,
>
> Peter
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] update probelm...

[Kanwei Li]

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/scripts/packed/jquery.jstore.js which remote deleted
> use (c)hanged version or (d)elete? interrupted!
>
> When I tried to do the update again...it says 'no changes found'
>
> But...after restarting my instance...I see that the changes did not get
> implemented.
>
> Is there a way to force this?
>
> Thanks in advance,
> Liisa
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] PostgreSQL issue: reserved keyword used as identifier

[Kanwei Li]

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 problem concerning the database. I'm currently trying
>> > to transfer my data from MySQL to PostgreSQL by writing a Perl script
>> > that would do the job.
>> >
>> > Here is the issue: In the "form_definition" table, one of the field
>> > identifiers is "desc", which is a reserved SQL keyword used for ordering
>> > values. Therefore, There's currently no way of making any query of the
>> > type "INSERT INTO table_name () VALUES (> > list>);" which is a big handicap in this context, since the order of the
>> > identifiers list we dynamically retrieve is not necessarily (and seldom)
>> > the right order.
>> >
>> > Is there a way to fix this issue without blowing everything up?
>>
>> You need to quote the identifiers.  A simple example using "desc" as a
>> column name:
>>
>> sdavis=# create table test_table(
>> id int,
>> desc varchar);
>> ERROR:  syntax error at or near "desc"
>> LINE 3: desc varchar);
>>         ^
>> sdavis=# create table test_table(
>> id int,
>> "desc" varchar);
>> CREATE TABLE
>>
>> Hope that helps.
>>
>> Sean
>
> Thanks, but I cheated by duplicating a little the information and it
> works fine. I use "insert into table values (...);".
>
> I still have problems transfering the data though. The script runs
> without growling but nothing is actually written in the target tables...
> I'll have to see that on monday now :/
>
> If I succeed, I'll let you know.
>
> Cheers,
> L-A
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Updating BLAST+ wrapper

[Kanwei Li]

Done the manual way
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Password input field for tools?

[Kanwei Li]

Well, it could be modified to never return a value back to the
interface after being set. Would that be sufficient?

On Mon, Apr 4, 2011 at 11:46 AM, Daniel Schmidt  wrote:
> Hello all!
>
> Thanks alot K! Although I have to admit, that it seems too insecure, at
> least for the tool I am currently working on. The password field is needed
> to connect to a database, which contains (sensitive) patient data. Revealing
> the password to someone else by accident when re-running a job could give
> him or her access to data he or she should have never access to.
> In spite 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 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:
>>>
>>> Hi all!
>>>
>>> Is there any way to use password input fields (">> type="password"...")
>>> with tools? A tools XML definition file only seems to support text and
>>> textarea fields. I already tried setting a tools parameter type to
>>> "password", which unfortunately results in an "Unknown tool parameter
>>> type
>>> 'password'". Trying "password="True"" (like "area="True"") does not
>>> result
>>> in an error, but the text field is still just a normal text field.
>>> I may be mistaken, as I am new to Python and Galaxy, but there already
>>> seems
>>> to be a PasswordField class and a TextField class, which both can be
>>> found
>>> in several files. Was the PasswordField class for tool parameters maybe
>>> disabled for a reason?
>>>
>>> Thanks!
>>> Daniel
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>
>>>  http://lists.bx.psu.edu/
>>>
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Updating BLAST+ wrapper

[Kanwei Li]

dhcp243253:galaxy-central kanwei$ hg transplant -s
~/peter/galaxy-central/ -b blast25
searching for changes
changeset:   5585:ab40f95393ec
branch:  blast25
parent:  5583:086c9c2c52b9
user:peterjc 
date:Mon Apr 04 12:12:11 2011 +0100
summary: Update tests for NCBI BLAST 2.2.25+ which fixed subject
ID in tabular output

apply changeset? [ynmpcq?]: y
changeset:   5586:124e4556f3c5
branch:  blast25
user:peterjc 
date:Mon Apr 04 14:44:52 2011 +0100
summary: Include optional parameters in BLASTP test to avoid KeyError

apply changeset? [ynmpcq?]: y
searching for changes
adding changesets
adding manifests
adding file changes
added 2 changesets with 4 changes to 4 files
dhcp243253:galaxy-central kanwei$ hg tip
changeset:   5338:124e4556f3c5
branch:  blast25
tag: tip
user:peterjc 
date:Mon Apr 04 14:44:52 2011 +0100
summary: Include optional parameters in BLASTP test to avoid KeyError

dhcp243253:galaxy-central kanwei$ hg push
pushing to https://kan...@bitbucket.org/galaxy/galaxy-central/
searching for changes
abort: push creates new remote branches: blast25!
(use 'hg push --new-branch' to 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 think it's because the parent of those changesets were before your
>> merge, so the branches got messed up
>
> But I haven't done any merge in this branch's history... It starts here,
> with James' latest commit to the trunk:
>
> https://bitbucket.org/galaxy/galaxy-central/changeset/086c9c2c52b9
> https://bitbucket.org/peterjc/galaxy-central/changeset/086c9c2c52b9
>
> Then I update the test files,
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec
>
> Then I update missing arguments in one test:
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5
>
> This seems to be confirmed by hg log,
>
> $ hg log --branch blast25
> changeset:   5586:124e4556f3c5
> branch:      blast25
> tag:         tip
> user:        peterjc 
> date:        Mon Apr 04 14:44:52 2011 +0100
> summary:     Include optional parameters in BLASTP test to avoid KeyError
>
> changeset:   5585:ab40f95393ec
> branch:      blast25
> parent:      5336:086c9c2c52b9
> user:        peterjc 
> date:        Mon Apr 04 12:12:11 2011 +0100
> summary:     Update tests for NCBI BLAST 2.2.25+ which fixed subject
> ID in tabular output
>
>
> Do you definitely have the latest code from galaxy-central in your
> repository? If you local copy is out of date that might explain things.
>
> Peter
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Password input field for tools?

[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 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:
> Hi all!
>
> Is there any way to use password input fields (" with tools? A tools XML definition file only seems to support text and
> textarea fields. I already tried setting a tools parameter type to
> "password", which unfortunately results in an "Unknown tool parameter type
> 'password'". Trying "password="True"" (like "area="True"") does not result
> in an error, but the text field is still just a normal text field.
> I may be mistaken, as I am new to Python and Galaxy, but there already seems
> to be a PasswordField class and a TextField class, which both can be found
> in several files. Was the PasswordField class for tool parameters maybe
> disabled for a reason?
>
> Thanks!
> Daniel
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>


passwordparam.patch
Description: Binary data
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Updating BLAST+ wrapper

[Kanwei Li]

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
>> galaxy-central base)
>
> I'm a bit puzzled and not an hg expert. Was there an error message?
>
> And for plan (B), what went wrong with using patch and the raw
> changes? Surely that should work?
> https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec/raw/galaxy-central-ab40f95393ec.diff
> https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5/raw/galaxy-central-124e4556f3c5.diff
>
> Peter
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Updating BLAST+ wrapper

[Kanwei Li]

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 transplant
>> or import the patches properly.
>>
>> K
>
> Hi Kanwei,
>
> I'm not sure why they won't transplant - they are both on this fresh
> branch from the trunk, with just these two commits so far:
>
> https://bitbucket.org/peterjc/galaxy-central/src/blast25
>
> Can you just merge that "blast25" branch?
>
> Alternatively, do the raw changesets help? First:
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec/raw/galaxy-central-ab40f95393ec.diff
>
> Then:
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5/raw/galaxy-central-124e4556f3c5.diff
>
> Peter
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Updating BLAST+ wrapper

[Kanwei Li]

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, 2011 at 6:28 PM, Peter Cock  
>>> wrote:
 Hi all,

 The NCBI have just released BLAST 2.2.25+ which includes some
 interesting new stuff of interest to the tabular output, ...
>>>
>>> One reason why I want to move to BLAST 2.2.25+ on our local
>>> machine is they fixed the subject IDs in tabular output, ...
>>
>> Hi Kanwei,
>>
>> Could you transplant or merge this commit please?
>> https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec
>>
>> It updates the test output files to work with BLAST 2.2.25+, which I
>> will be using locally due to several important bug fixes. As you don't
>> offer BLAST+ on the Penn State server I don't expect this to cause
>> you any problems.
>>
>> Also (and unrelated to this change), do you see this from the test suite?
>>
>> $ ./run_functional_tests.sh -id ncbi_blastp_wrapper
>> ...
>> ==
>> ERROR: NCBI BLAST+ blastp ( ncbi_blastp_wrapper ) > Test-1
>> --
>> Traceback (most recent call last):
>>  File 
>> "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py",
>> line 155, in test_tool
>>    self.do_it( td )
>>  File 
>> "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py",
>> line 71, in do_it
>>    page_inputs =
>> self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs)
>>  File 
>> "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py",
>> line 122, in __expand_grouping
>>    elif isinstance(declared_inputs[value.name], str):
>> KeyError: 'blast_type'
>
> Solved, it seems I can't omit any parameters in the  and expect
> the defaults to be used. This doesn't seem desirable (new bug?), but the
> quick fix is to add a few lines to the test. Could you commit this too:
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5
>
> Thanks,
>
> Peter
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Default value for data_column not working?

[Kanwei Li]

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 output).
>
> I want the user to be able to choose a column number (from one of the
> input files), but I have a default column in mind. However, Galaxy
> doesn't seem to obey the default column number:
>
>    
>        
>        
>         multiple="False" numerical="False" value="1" label="Column containing
> query ID" help="This is column 1 in standard BLAST tabular output" />
>         multiple="False" numerical="False" value="2" label="Column containing
> match ID" help="This is column 2 in standard BLAST tabular output"/>
>         multiple="False" numerical="False" value="12" label="Column containing
> containing score to rank on" help="The bitscore is column 12 in
> standard BLAST tabular output"/>
>    
>
> I've tried giving the default column value numerically (as shown), and
> also using value="c2" etc. Regardless, Galaxy just defaults to the
> first column.
>
> Is this a bug, or am I doing something wrong?
>
> Thanks,
>
> Peter
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] galaxy python crash with segfault in csamtools.so when using tracks

[Kanwei Li]

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
> invoked:
>
> Mar 21 17:12:14 bat4 kernel: [4080861.873724] python[14319]: segfault at
> 45cfb1e8 ip 7f1559865444 sp 7f155192d1b0 error 4 in
> csamtools.so[7f1559837000+55000]
>
>
> Anyone have advice on where to start investigating?
>
> Thanks,
>
> JJ
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] History information popup broken on library entries?

[Kanwei Li]

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 history, that the
> little 'i' information icon's black popup window isn't working for these
> datasets. All it says is 'Could not find the job for this dataset.'
>
> This appears to affect multiple file types (FASTA and BAM tested)
> and both files copied into Galaxy or linked to at import.
>
> I'm using the current latest code from galaxy-central,
> https://bitbucket.org/galaxy/galaxy-central/changeset/e39495db6071
>
> This also seems to affect http://test.g2.bx.psu.edu/ and also
> http://main.g2.bx.psu.edu/
>
> Can anyone confirm this behaviour? I'm using Firefox on the Mac,
> but I doubt that is relevant.
>
> Peter
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Metadata recursion error with empty tabular file (with patch)

[Kanwei Li]

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 wrapper finish method failed
> Traceback (most recent call last):
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/runners/local.py",
> line 125, in run_job
>job_wrapper.finish( stdout, stderr )
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/__init__.py",
> line 578, in finish
>dataset.set_peek()
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py",
> line 690, in set_peek
>return self.datatype.set_peek( self, is_multi_byte=is_multi_byte )
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py",
> line 227, in set_peek
>data.Text.set_peek( self, dataset, line_count=line_count,
> is_multi_byte=is_multi_byte )
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py",
> line 431, in set_peek
>self.set_peek(dataset)
> ...
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py",
> line 227, in set_peek
>data.Text.set_peek( self, dataset, line_count=line_count,
> is_multi_byte=is_multi_byte )
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py",
> line 431, in set_peek
>self.set_peek(dataset)
> ...
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py",
> line 227, in set_peek
>data.Text.set_peek( self, dataset, line_count=line_count,
> is_multi_byte=is_multi_byte )
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py",
> line 419, in set_peek
>dataset.peek = get_file_peek( dataset.file_name,
> is_multi_byte=is_multi_byte )
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py",
> line 628, in get_file_name
>return self.dataset.get_file_name()
>  File
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py",
> line 515, in get_file_name
>return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id )
> )
>  File "/usr/local/lib/python2.6/posixpath.py", line 348, in abspath
>return normpath(path)
>  File "/usr/local/lib/python2.6/posixpath.py", line 314, in normpath
>slash, dot = (u'/', u'.') if isinstance(path, unicode) else ('/', '.')
> RuntimeError: maximum recursion depth exceeded while calling a Python
> object
>
>
> >From the trace, two set_peek methods are calling each other in a loop. I
> deduced
> the problem was an empty tabular files, where
> dataset.metadata.data_lines is zero,
> but the test should really have been for None. Please review and apply
> this patch
> which appears to correctly resolve the issue:
>
>
> diff -r 9fae539215be lib/galaxy/datatypes/data.py
> --- a/lib/galaxy/datatypes/data.py  Fri Mar 18 11:46:48 2011 +
> +++ b/lib/galaxy/datatypes/data.py  Fri Mar 18 11:49:05 2011 +
> @@ -422,7 +422,7 @@
> dataset.peek = get_file_peek( dataset.file_name,
> is_multi_byte=is_multi_byte )
> if line_count is None:
> # See if line_count is stored in the metadata
> -if dataset.metadata.data_lines:
> +if dataset.metadata.data_lines is not None:
> dataset.blurb = "%s %s" % ( util.commaify(
> str(dataset.metadata.data_lines) ),
> inflector.cond_plural(dataset.metadata.data_lines, "line") )
> else:
> # Number of lines is not known ( this should not
> happen ), and auto-detect is
>
>
>
> Thanks,
>
> Peter
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] about bx-python and bigwig

[Kanwei Li]

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:

> Hello James,
>
> On Mar 8, 2011, at 1:23 AM, James Taylor wrote:
>
> Davide, see bx.bbi.bigwig_file.BigWigFile
>
>
> I'm trying to... :-)
>
> Implemented in Cython, there is also some BigBed support with a common
> class (bbi_file) for the indexing and aggregation pieces.
>
> This is currently read only. Also, not tested exhaustively on different
> types of bigwig, but I believe we have most cases correct.
>
>
> read only is fine for me (at least at the moment). I see the method to get
> data from a bigwig file is BigWigFile.query(), is it?
> What is the summary_size one must specify? Data are returned as statistics
> of the region between chr:start-end, the number of statistics is given by
> summary_size. In my mind the summary_size could be the number of "chunks"
> between start and end. Unfortunately I see that I can specify summary_size >
> (end - start) hence I don't know what summary_size is :-)
>
> d
>
>
>
> /*
> Davide Cittaro, PhD
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007
> e-mail: davide.citt...@ifom-ieo-campus.it
> */
>
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?

[Kanwei Li]

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 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 Fri, Feb 18, 2011 at 10:50 PM, Kanwei Li  wrote:
> > The empty tool pane issue for IE is now fixed on tip as well.
> > Thanks,
> > -K
> >
>
> Hi Kanwei,
>
> I presume this was the fix for the peep view not working on IE7,
> https://bitbucket.org/galaxy/galaxy-central/changeset/1dfad17e81a8
>
> That doesn't seem to have been included in the latest galaxy-dist
> release.
>
> I've tried both main.g2.bx.psu.edu and test.g2.bx.psu.edu with
> IE7 and the peep view is still unchanged. Should the test machine
> be working? Perhaps there is a caching problem...
>
> Also, when using either main.g2.bx.psu.edu or test.g2.bx.psu.edu
> with IE7 I am now getting a JavaScript error when I click on any tool:
>
> Line: 52
> Error: Object doesn't support this property or method
>
> Offending line:
>
> var section_title =
>
> $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text().trim();
>
> Context:
>
> // Log clicks on tools.
> $("div.toolTitle > a").click( function()
> {
>var tool_title = $(this).attr('id').split("-")[1];
>var section_title =
>
> $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text().trim();
>var search_active =
> $(this).parents("div.toolTitle").hasClass("search_match");
>
>// Log action.
>galaxy_async.log_user_action("tool_menu_click." + tool_title,
> section_title,
>JSON.stringify({"search_active" : search_active}));
> });
>
> This may be unrelated, but you said you'd been working on the tool
> pane too, so I'm mentioning it here rather than starting a new thread
> or filing a bug..
>
> Peter
>
___
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?

[Kanwei Li]

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
___
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] sorting bam

[Kanwei Li]

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
> please?
>
> ___
> To manage your subscriptions to this and other Galaxy lists, please use the
> interface at:
>
>  http://lists.bx.psu.edu/
>
___
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?

[Kanwei Li]

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 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 Mon, Jan 31, 2011 at 1:06 PM, Peter wrote:
>
>> On Mon, Jan 31, 2011 at 5:54 PM, Leandro Hermida
>>  wrote:
>> > Hi,
>> >
>> > In IE go to Tools -> Internet Options -> Advanced Tab, then under
>> Browsing
>> > section:
>> >
>> > Uncheck "Disable Script debugging (Internet Explorer)
>> > Uncheck "Disable Script debugging (Other)
>> > Check Display a notification about every script error
>> >
>> > Then you will see the Javascript error when you try to reload the Galaxy
>> > page and then try to expand a history item.  I would help debug the
>> Galaxy
>> > IE issues but I am at work and cannot change these settings on my work
>> > computer (the are grey out :( )
>> >
>> > -Leandro
>>
>> I had done ""Disable Script debugging (Internet Explorer)" and "Display
>> a notification about every script error", but not "Disable Script
>> debugging
>> (Other)". However I still don't see any javascript error when using
>> Galaxy.
>>
>> Peter
>>
>> ___
>> galaxy-dev mailing list
>> galaxy-dev@lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>
>
___
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?

[Kanwei Li]

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 Mon, Jan 31, 2011 at 1:06 PM, Peter  wrote:

> On Mon, Jan 31, 2011 at 5:54 PM, Leandro Hermida
>  wrote:
> > Hi,
> >
> > In IE go to Tools -> Internet Options -> Advanced Tab, then under
> Browsing
> > section:
> >
> > Uncheck "Disable Script debugging (Internet Explorer)
> > Uncheck "Disable Script debugging (Other)
> > Check Display a notification about every script error
> >
> > Then you will see the Javascript error when you try to reload the Galaxy
> > page and then try to expand a history item.  I would help debug the
> Galaxy
> > IE issues but I am at work and cannot change these settings on my work
> > computer (the are grey out :( )
> >
> > -Leandro
>
> I had done ""Disable Script debugging (Internet Explorer)" and "Display
> a notification about every script error", but not "Disable Script debugging
> (Other)". However I still don't see any javascript error when using Galaxy.
>
> Peter
>
> ___
> galaxy-dev mailing list
> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
___
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Problem upgrading DB from 72 to 73 (SQLite)

[Kanwei Li]

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.sh upgrade
>> 72 -> 73...
>>
>> Migration script to add 'ldda_parent_id' column to the
>> implicitly_converted_dataset_association table.
>>
>> Adding ldda_parent_id column to
>> implicitly_converted_dataset_association table failed: SQLite does not
>> support ALTER TABLE ADD FOREIGN KEY; see
>> http://www.sqlite.org/lang_altertable.html
>> done
>>
>
> Concerningly, although the upgrade says it fails, it looks like some
> of it worked:
>
> $ sh manage_db.sh db_version
> 73
>
> Shouldn't each update step be one big transaction that gets rolled
> back to leave things in a known state (in this case, schema version
> 72)?
>
> Peter
> ___
> galaxy-dev mailing list
> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev

Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

[Kanwei Li]

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-central/changeset/aa82d8273063
>
> Cope with errors on stderr,
> https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c
>
> Ensure blast jobs get killed,
> https://bitbucket.org/peterjc/galaxy-central/changeset/607b7268693a
>
> Peter
>
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev

Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?

[Kanwei Li]

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 preferred over
>> ${param.get_fields( 'path' )}?
>>
>> Thanks,
>>
>> Dan
>
> That looks nicer to type in the XML wrapper, but I am not
> overly bothered. Could we use either syntax for things like
> filters and conditional checks (in other parameters)?
>
> Peter
> ___
> galaxy-dev mailing list
> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev