On Thu, Feb 23, 2012 at 12:00 PM, <galaxy-dev-request@lists.bx.psu.edu> wrote:

Send galaxy-dev mailing list submissions to
galaxy-dev@lists.bx.psu.edu

To subscribe or unsubscribe via the World Wide Web, visit
http://lists.bx.psu.edu/listinfo/galaxy-dev
or, via email, send a message with subject or body 'help' to
galaxy-dev-request@lists.bx.psu.edu

You can reach the person managing the list at
galaxy-dev-owner@lists.bx.psu.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-dev digest..."

HEY! This is important! If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you are responding to.

Why?
1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.

Today's Topics:

1. Re: Error 500 when trying to execute a workflow with the API
(Anthonius deBoer)
2. Re: Error 500 when trying to execute a workflow with the API
(dannonbaker@me.com)
3. Re: Splitting large jobs over multiple nodes/CPUs? (Peter Cock)
4. Re: Splitting large jobs over multiple nodes/CPUs?
(dannonbaker@me.com)
5. FastX tools (Borrone, James)
6. snpEff: html report is not displaying after update
(Jennifer Jackson)
7. R scripts for DESeq (Jennifer Jackson)
8. limited tool shed browse (David Hoover)
9. Re: FastX tools (Peter Cock)
10. Re: limited tool shed browse (Greg Von Kuster)
11. Re: R scripts for DESeq (Vipin TS)
12. Re: limited tool shed browse (David Hoover)
13. Re: limited tool shed browse (Greg Von Kuster)
14. Re: How to learn about new tools in the official Tool Shed
(Jennifer Jackson)
15. Re: R scripts for DESeq (Liusong Yang)
16. Re: R scripts for DESeq (Greg Von Kuster)
17. Re: uploads stuck in history (Bossers, Alex)
18. Re: R scripts for DESeq (Christian Cole)
19. Re: R scripts for DESeq (Vipin TS)
20. Re: Splitting large jobs over multiple nodes/CPUs? (Peter Cock)

----------------------------------------------------------------------

Message: 1
Date: Wed, 22 Feb 2012 18:09:40 +0000 (GMT)
From: Anthonius deBoer <thondeboer@me.com>
To: Dannon Baker <dannonbaker@me.com>
Cc: Galaxy-dev <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Error 500 when trying to execute a workflow
with the API
Message-ID: <ddf015a9-c563-e45d-cb06-af4780110d91@me.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Huh? I have many string inputs to some particular workflow steps...Those are parameters etc that need to be entered or chosen from a dropdown..How would we deal with those kinds of entries into a workflow in the API? Or do all of them have to be pre-set?

Thanks

Thon?

On Feb 21, 2012, at 04:21 PM, Dannon Baker <dannonbaker@me.com> wrote:

> There is no string input. If the string you're looking for is, say, the name of a dataset what you'd do is make separate calls to the history and workflow API.
>
> For example, if you had a history "My important history", and a dataset "My input dataset", and no knowledge of the id's (as you shouldn't' have to have, externally), it'd be three separate calls. One to list histories, then you would programmatically grab the one you want ("My important history") and the ID associated with it. Then you'd make a call to grab the contents of that history, from which you could extract the id of the dataset you had the name of. And from there you know how to execute a workflow with that id (hda, in this case).
>
> -Dannon
>
>
>
>
> On Feb 21, 2012, at 7:13 PM, thondeboer@me.com wrote:
>
> > One more question...
> > How do I pass a string value to one of the workflow input steps?
> > Is there an equivalent of ldda and hda, maybe "str"..
> >
> > So 38=str="Some value"
> >
> > Where could I find a list of the expected dataset sources?
> >
> > Thanks
> >
> > Thon
> >
> > On Feb 21, 2012, at 03:46 PM, Dannon Baker <dannonbaker@me.com> wrote:
> >
> >> Hi Thon,
> >>
> >> You have the right idea about what's going wrong here. Galaxy is trying to pull up a library dataset with the ID you specify, but it doesn't exist.
> >>
> >> In this context, src refers to the 'type' of dataset input id, more specifically whether it's from a history or library. 'hda' indicates that the dataset is from a history, and 'ldda' is what you'll most likely use in the case of a library dataset. If you browse the history and library API functionality, you'll see other methods for explicitly grabbing these ids.
> >>
> >> My hunch is that you have an id from a history and that you should swap ldda to hda and give it another shot. Definitely let me know if you run into more issues, though, and I'll help figure out what's going on.
> >>
> >> -Dannon
> >>
> >> On Feb 21, 2012, at 6:22 PM, thondeboer@me.com wrote:
> >>
> >> > Hi,
> >> >
> >> > I tried to run a workflow with the API, but get an Error 500 when I try to run the WF...The paster.log shows the following error...
> >> >
> >> > $ workflow_execute.py 92cc01ed93dc0f0fc91e3ded35497c0a http://srp106:8080/api/workflows ebfb8f50c6abde6d 'TEST the API' '1=ldda=7c5ebce002fc9d5c'
> >> >
> >> >
> >> > Paster.log
> >> > galaxy.web.framework ERROR 2012-02-21 14:36:33,067 Uncaught exception in exposed API method:
> >> > Traceback (most recent call last):
> >> > File "/home/tdeboer/code/galaxy-central/lib/galaxy/web/framework/__init__.py", line 145, in decorator
> >> > return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True )
> >> > File "/home/tdeboer/code/galaxy-central/lib/galaxy/web/api/workflows.py", line 123, in create
> >> > hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
> >> > AttributeError: 'NoneType' object has no attribute 'to_history_dataset_association'
> >> > 172.16.108.6 - - [21/Feb/2012:14:36:32 -0700] "POST /api/workflows?key=92cc01ed93dc0f0fc91e3ded35497c0a HTTP/1.1" 500 - "-" "Python-urllib/2.6"
> >> >
> >> >
> >> > Any ideas?
> >> >
> >> > Also...I had a hard time finding out what I should use for the dataset source parameter "src" in "step=src=dataset_id" and just tried ldda, but would hope there is a little info on what this hda and ldda is?
> >> >
> >> > Thanks,
> >> >
> >> > Thon
> >> > ___________________________________________________________
> >> > 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/
> >>
> >> One
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120222/eb345fc3/attachment-0001.html>

------------------------------

Message: 2
Date: Wed, 22 Feb 2012 18:20:08 +0000 (GMT)
From: dannonbaker@me.com
To: Anthonius deBoer <thondeboer@me.com>
Cc: Galaxy-dev <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Error 500 when trying to execute a workflow
with the API
Message-ID: <a7da2bba-ef10-e9f0-b12d-99e7a353c6fb@me.com>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

Ahh, I see what you're asking. ?I thought you were referring to providing dataset inputs by name, my mistake.

Currently running workflows through the API doesn't support defining inputs other than datasets, that is, it expects workflows to be fully pre-defined with nothing 'set at runtime' other than the input datasets.

That said, this is something that's definitely on my plate to add, unless the community gets to it first, in which case I'll happily accept a pull request :)

-Dannon

On Feb 22, 2012, at 10:11 AM, Anthonius deBoer <thondeboer@me.com> wrote:

Huh? I have many string inputs to some particular workflow steps...Those are parameters etc that need to be entered or chosen from a dropdown..How would we deal with those kinds of entries into a workflow in the API? Or do all of them have to be pre-set?

Thanks

Thon

On Feb 21, 2012, at 04:21 PM, Dannon Baker <dannonbaker@me.com> wrote:

There is no string input. If the string you're looking for is, say, the name of a dataset what you'd do is make separate calls to the history and workflow API.

For example, if you had a history "My important history", and a dataset "My input dataset", and no knowledge of the id's (as you shouldn't' have to have, externally), it'd be three separate calls. One to list histories, then you would programmatically grab the one you want ("My important history") and the ID associated with it. Then you'd make a call to grab the contents of that history, from which you could extract the id of the dataset you had the name of. And from there you know how to execute a workflow with that id (hda, in this case).

-Dannon

On Feb 21, 2012, at 7:13 PM, thondeboer@me.com wrote:

> One more question...
> How do I pass a string value to one of the workflow input steps?
> Is there an equivalent of ldda and hda, maybe "str"..
>
> So 38=str="Some value"
>
> Where could I find a list of the expected dataset sources?
>
> Thanks
>
> Thon
>
> On Feb 21, 2012, at 03:46 PM, Dannon Baker <dannonbaker@me.com> wrote:
>
>> Hi Thon,
>>
>> You have the right idea about what's going wrong here. Galaxy is trying to pull up a library dataset with the ID you specify, but it doesn't exist.
>>
>> In this context, src refers to the 'type' of dataset input id, more specifically whether it's from a history or library. 'hda' indicates that the dataset is from a history, and 'ldda' is what you'll most likely use in the case of a library dataset. If you browse the history and library API functionality, you'll see other methods for explicitly grabbing these ids.
>>
>> My hunch is that you have an id from a history and that you should swap ldda to hda and give it another shot. Definitely let me know if you run into more issues, though, and I'll help figure out what's going on.
>>
>> -Dannon
>>
>> On Feb 21, 2012, at 6:22 PM, thondeboer@me.com wrote:
>>
>> > Hi,
>> >
>> > I tried to run a workflow with the API, but get an Error 500 when I try to run the WF...The paster.log shows the following error...
>> >
>> > $ workflow_execute.py 92cc01ed93dc0f0fc91e3ded35497c0a http://srp106:8080/api/workflows ebfb8f50c6abde6d 'TEST the API' '1=ldda=7c5ebce002fc9d5c'
>> >
>> >
>> > Paster.log
>> > galaxy.web.framework ERROR 2012-02-21 14:36:33,067 Uncaught exception in exposed API method:
>> > Traceback (most recent call last):
>> > File "/home/tdeboer/code/galaxy-central/lib/galaxy/web/framework/__init__.py", line 145, in decorator
>> > return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True )
>> > File "/home/tdeboer/code/galaxy-central/lib/galaxy/web/api/workflows.py", line 123, in create
>> > hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
>> > AttributeError: 'NoneType' object has no attribute 'to_history_dataset_association'
>> > 172.16.108.6 - - [21/Feb/2012:14:36:32 -0700] "POST /api/workflows?key=92cc01ed93dc0f0fc91e3ded35497c0a HTTP/1.1" 500 - "-" "Python-urllib/2.6"
>> >
>> >
>> > Any ideas?
>> >
>> > Also...I had a hard time finding out what I should use for the dataset source parameter "src" in "step=src=dataset_id" and just tried ldda, but would hope there is a little info on what this hda and ldda is?
>> >
>> > Thanks,
>> >
>> > Thon
>> > ___________________________________________________________
>> > 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/
>>
>> One

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120222/65629a52/attachment-0001.html>

------------------------------

Message: 3
Date: Wed, 22 Feb 2012 18:59:42 +0000
From: Peter Cock <p.j.a.cock@googlemail.com>
To: "Fields, Christopher J" <cjfields@illinois.edu>
Cc: "<galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Splitting large jobs over multiple
nodes/CPUs?
Message-ID:
<CAKVJ-_7FpBDdur9pY2+=4pN+wzXpc7UmpA8o0OC5JYpQe4L7RQ@mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

On Thu, Feb 16, 2012 at 9:02 PM, Peter wrote:
> On Thu, Feb 16, 2012 at 6:42 PM, Chris wrote:
>> On Feb 16, 2012, at 12:24 PM, Peter wrote:
>>> I also need to look at merging multiple BLAST XML outputs,
>>> but this is looking promising.
>>
>> Yep, that's definitely one where a simple concatenation
>> wouldn't work (though NCBI used to think so, years ago?)
>
> Well, given the NCBI's historic practise of producing 'XML'
> output which was the concatenation of several XML files,
> some tools will tolerate this out of practicality - the Biopython
> BLAST XML parser for example.
>
> But yes, some care is needed over the header/footer to
> ensure a valid XML output is created by the merge. This
> may also require renumbering queries... I will check.

Basic BLAST XML merging implemented and apparently working:
https://bitbucket.org/peterjc/galaxy-central/changeset/ebf65c0b1e26

This does not currently attempt to remap the iteration
numbers or automatically assigned query names, e.g.
you can have this kind of thing in the middle of the XML
at a merge point:

<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>Query_1</Iteration_query-ID>

That isn't a problem for some tools, e.g. my code in
Galaxy to convert BLAST XML to tabular, but I suspect
it could cause trouble elsewhere. If anyone has specific
suggestions for what to test, that would be great.

If this is an issue, then the merge code needs a little
more work to edit these values.

I think the FASTA split code could be reviewed for
inclusion though. Dan - do you want to look at that?
Would a clean branch help?

Peter

------------------------------

Message: 4
Date: Wed, 22 Feb 2012 19:07:54 +0000 (GMT)
From: dannonbaker@me.com
To: Peter Cock <p.j.a.cock@googlemail.com>
Cc: "<galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Splitting large jobs over multiple
nodes/CPUs?
Message-ID: <ee09237b-f763-68fa-91f2-a566a1d0f5f8@me.com>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

Awesome, I'll take a look. ?And, if you're able to pull it together easily enough, clean branches are always nice.

-Dannon

On Feb 22, 2012, at 10:59 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Basic BLAST XML merging implemented and apparently working:
https://bitbucket.org/peterjc/galaxy-central/changeset/ebf65c0b1e26

This does not currently attempt to remap the iteration
numbers or automatically assigned query names, e.g.
you can have this kind of thing in the middle of the XML
at a merge point:

<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>Query_1</Iteration_query-ID>

That isn't a problem for some tools, e.g. my code in
Galaxy to convert BLAST XML to tabular, but I suspect
it could cause trouble elsewhere. If anyone has specific
suggestions for what to test, that would be great.

If this is an issue, then the merge code needs a little
more work to edit these values.

I think the FASTA split code could be reviewed for
inclusion though. Dan - do you want to look at that?
Would a clean branch help?

Peter
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120222/f77daafa/attachment-0001.html>

------------------------------

Message: 5
Date: Tue, 21 Feb 2012 11:49:17 -0600
From: "Borrone, James" <james.w.borrone@okstate.edu>
To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] FastX tools
Message-ID:
<98318B2494241248846FE45D0D02B6EF015729D4E51F@STWEXE2.ad.okstate.edu>
Content-Type: text/plain; charset="us-ascii"

hello,

I am trying to use the FastX tools on the Main server to trim and manipulate FASTQ files extracted directly from an sff file (again using the main galaxy web server). In using Clip and the Reverse compliment tools, I get the following error:

An error occurred running this job: fastx_reverse_complement: (or fastx_clip) found invalid nucleotide sequence (gactGCGACTCACGTACAGCAATGCACATACTATATTATATC) on line 2

gzip: stdout: Broken pipe

I have downloaded the fastx tool kit and installed it locally on my computer and experience the same problem, so I suspect that it is a format error. My fastq file looks like this:

@HA3HTSF01AH1DX
gactGCGACTCACGTACAGCAATGCACATACTATATTATATCAACCtcacaacacactacacgacacacaggagagagnnn
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFAAB88..--,,/152///0///14,,,,///00//////!!!
@HA3HTSF01B3YMI
gactTTTGGGATTTGTTAACTTAGTTTGTAGGTGGTGGTTATAATGTTTGTGTGGTGTTATGTTTGGTGTAGTGttttgggttggtttgtattatttgtggatttggagttcgtgggtaggcaaggcacactagggggattaggtngngtnntntntttnntgntgtgntctgtgtggttgtggtgattttttactttgagtgttttgcgatttgggtgtagtaattagtcggtttttacgtaatttttaggttttgtggggttttgatttgggtttaggttttaatgcttttgatggtgggtgggggttcttacacgggtttaggttagagttggttgggctatgcatatgggtgtttgggggtttcttatttgggatgttttaggtgccatgtaatatttgtttangcgagtcgttttggttcttttaattttattacttgttttaggattgtttttaggtttaatagaaaatttntgactttttttaagggtttgggttaacatggcagttttttggggtttgggaattttttagtacgttagtttaggttaggttggttaggttagttagttagttgttgttggttgttagttgtttggttggttaggtttggttttgggttttgggttttaggttttnnnnnnnnnnn
+
??<//00==BA@>>A=BBCFDD:9444GGIIIIEIIIIIIIIIIG9444GGIIEGFDDEIB8443?;:;;@880----0000088001A@EEEECCCGEEEEB@?<<=900033--,/7..000511156675,,,,,,01/,,,!5!11!!0!,!,//!!40!0588!6665511111/,,,,/11,,,,,,,,--/:688<7<77>>>;333---13511///53////////111132.11,,,,,,,,,,,,/,444666772886::43.,,,..,,,,,,066....565...,,,,111....11111.,,,,,,,.2222442,,--------8777:::99900-2----,,,,,,,,-,,,233,,-774-----099564422000-,,,,-,,,,!-02222223433..,,.33,,,,22226//5888,,,,,,446622---..0,,,,0110220000,,,!.222,++++++++---001/-1--..33331001------++++++++++00++++++++++++++---00------+++++++++011111000000------0+++00000+++00--+++00----+++00000--++++0++++++-+++++++--++++!!!!!!!!!!!
@HA3HTSF01BHUOB
gactCATGCTTCAGATCAAGCAAGTCTTCGCTGACTACGTGCGCCATCGCCGCGAGGcgcagcacggaagtaggagcggcgtcagctcgccaacatgacgcgcgaattccacgaagagacacaaagacaccttgggaacctcttcaagtacgcggaggagaagatacgccgcgtcgcacaggaggagcacaaggcacacaggggataggnn
+
IIIIIIIIIIIGIIIGG@@@H>>>@IIIIIIIIIIIIIIIIIIIIIIIIEECGGE74426<AA812211/5/111/53385;::;AE>?330113==AACCC<=993333923333<DEGHF:::GIIIIIIIGIIIFCCEBB?:99<9;??=?99//053337<456333;?D@@<;==?943355@@@998895546:4444:4...!!
@HA3HTSF01ASNA7
gactATTGATATATTGCAACAGCTATCCAAATACACAAATATAATACTTGTTATAGGCAAATGCGACATTTTTGAGGCGAGTGAGTTGTTGCAATATATCAAtagtcgtgggaggcaaggcacacaggggatagg
+
IIIIIIIIIIIIIIIIIIIIIIIIIC<<111?1G??111D5IIIIIIIIIIIIIIIIIBBBIIIDIC?00000BBDCFCFFIIIIIIHHHIIIIIHHHIIIIIIIIIHH555GHIIIIIIIIIIIIFHHHIIIII

Can someone tell me what the format should be? I have tried converting the fastq file into a different format, to no avail. And I have extracted the FASTA and FASTA.qual files directly from the sff file, recombined them together, and still had the program fail to clip or reverse compliment the sequences.

So, i am at a loss as to what the format should look like. All of the extractions were done directly on the sff file uploaded to galaxy.

Thanks

James Borrone

------------------------------

Message: 6
Date: Wed, 22 Feb 2012 12:36:39 -0800
From: Jennifer Jackson <jen@bx.psu.edu>
To: Praveen Raj Somarajan <Praveen.s@ocimumbio.com>, Galaxy Dev
<galaxy-dev@bx.psu.edu>
Cc: galaxy-user <galaxy-user@lists.bx.psu.edu>,
"closeticket@galaxyproject.org" <closeticket@galaxyproject.org>
Subject: [galaxy-dev] snpEff: html report is not displaying after
update
Message-ID: <4F4551D7.2080504@bx.psu.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello Raj,

This tool is from the Tool Shed and is maintained by the tool author. To
contact them about functionality or problems, go to the Tool Shed at
http://toolshed.g2.bx.psu.edu/, locate the repository (search by
'snpEff'), click on the name, in the the top far right corner locate the
pull down menu "Repository Actions". Select "Contact repository owner"
to send them a message.

There have been many updates to Galaxy recently and it is possible that
one of these had an impact on this tool. I am going to send your email
to galaxy-dev@bx.psu.edu, to see if anyone else has had problems with
this tool since the last distribution update.

You may be asked to provide more information (be as specific as you
can): the hg pull #, any customizations, python version, etc.

Regards,

Jen
Galaxy team

On 2/14/12 8:28 PM, Praveen Raj Somarajan wrote:
> Hi All,
>
> I updated galaxy recently to the latest version. Everything looks fine,
> except snpEff report html view. It was displaying properly (all tables
> and summary values) before the update, but the summary values are not
> displaying after the update. A sample screen-shot is attached for your
> reference. Could you please figure out this issue?
>
> When I ran the same on command line, the reports were generated
> correctly. I assume, something (datatypes or preview) has changed by the
> update. Please let me know the work around on this?
>
> Secondly, as we know, snpEff also generates a gene-wise annotation file
> along with other results, but somehow we cannot access this file through
> Galaxy. Though we see the link in the html report, but it seems the path
> is broken.
>
> Let me know your suggestions.
>
> Best,
>
> Raj
>
>
> ------------------------------------------------------------------------
> This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended
> solely for the use of the addressee(s). If you are not the intended
> recipient, please notify the sender by e-mail and delete the original
> message. Further, you are not to copy, disclose, or distribute this
> e-mail or its contents to any other person and any such actions that are
> unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken
> every reasonable precaution to minimize this risk, but is not liable for
> any damage you may sustain as a result of any virus in this e-mail. You
> should carry out your own virus checks before opening the e-mail or
> attachment.
> The information contained in this email and any attachments is
> confidential and may be subject to copyright or other intellectual
> property protection. If you are not the intended recipient, you are not
> authorized to use or disclose this information, and we request that you
> notify us by reply mail or telephone and delete the original message
> from your mail system.
>
> OCIMUMBIO SOLUTIONS (P) LTD
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> 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/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

------------------------------

Message: 7
Date: Wed, 22 Feb 2012 12:53:05 -0800
From: Jennifer Jackson <jen@bx.psu.edu>
To: Galaxy Dev <galaxy-dev@bx.psu.edu>
Cc: Liusong Yang <liusongyang2009@gmail.com>
Subject: [galaxy-dev] R scripts for DESeq
Message-ID: <4F4555B1.2080205@bx.psu.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Lisa,

I am going to send your question over to the galaxy-dev@bx.psu.edu
mailing list so that the development community can offer feedback.
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-cloud_instance.2C_or_development_thread

Th galaxy-user list is primarily for tool/data usage on the Galaxy
public server.
http://wiki.g2.bx.psu.edu/Mailing%20Lists

Thanks,

Jen
Galaxy team

-------- Original Message --------
Subject: [galaxy-user] R scripts for DESeq
Date: Tue, 21 Feb 2012 23:25:35 -0500
From: Liusong Yang <liusongyang2009@gmail.com>
To: galaxy-user@lists.bx.psu.edu

Hello,

I am planning to put DESeq into galaxy. I am a newcomer for both
Galaxy and R. I have already read all of the related discussion in
this group. I also noticed that there are r_wrapper.sh and DESeq.xml
added into galaxy recently under the path of tools.

These lines are from r_wrapper.sh.

### Run R providing the R script in $1 as standard input and passing
### the remaining arguments on the command line

I guess this means we need to give the DESeq R script to the wrapper
as standard input. My question is where or what is the DESeq R
scripts? I installed R and DESeq package, but I can not fund anything
like DESeq.R or something similar? I feel so confusing now. Any
comments or suggestions would be absolutely appreciated!

Thanks

Lisa
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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/

------------------------------

Message: 8
Date: Wed, 22 Feb 2012 16:02:06 -0500
From: David Hoover <hooverdm@helix.nih.gov>
To: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: [galaxy-dev] limited tool shed browse
Message-ID: <B2CF38F2-4EDB-4454-B6D0-2B68874B8AFE@helix.nih.gov>
Content-Type: text/plain; charset="us-ascii"

When I click on Admin->'Search and browse tool sheds'->'Galaxy main tool shed', it shows the first page of Valid repositories. However, clicking '2', '3', '4', or 'Show All' has no effect. I can only display the first page of repositories.

However, if I search for valid tools using the menu under 'Galaxy main tool shed', I can get to any of the repositories listed at the Galaxy main toolshed.

Is this a bug or a feature?

David Hoover
Helix Systems Staff

------------------------------

Message: 9
Date: Wed, 22 Feb 2012 21:02:15 +0000
From: Peter Cock <p.j.a.cock@googlemail.com>
To: "Borrone, James" <james.w.borrone@okstate.edu>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] FastX tools
Message-ID:
<CAKVJ-_74DgX8Jt2ZK7tCaeEUeysz5JOh--RENck1OWxpwKWmTA@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Tue, Feb 21, 2012 at 5:49 PM, Borrone, James
<james.w.borrone@okstate.edu> wrote:
> hello,
>
> I am trying to use the FastX tools on the Main server to trim and manipulate FASTQ files extracted directly from an sff file (again using the main galaxy web server). ?In using Clip and the Reverse compliment tools, I get the following error:
>
> An error occurred running this job: fastx_reverse_complement: (or fastx_clip) found invalid nucleotide sequence (gactGCGACTCACGTACAGCAATGCACATACTATATTATATC) on line 2
>

When you turn the SFF into FASTQ, ask for the trimmed reads. That
will remove the lower case nucleotides.

Peter

------------------------------

Message: 10
Date: Wed, 22 Feb 2012 16:07:50 -0500
From: Greg Von Kuster <greg@bx.psu.edu>
To: David Hoover <hooverdm@helix.nih.gov>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] limited tool shed browse
Message-ID: <190D599F-5C9F-4F1F-90BF-B99F8DCB8CEB@bx.psu.edu>
Content-Type: text/plain; charset=us-ascii

Hi David,

I cannot reproduce this behavior from my local Galaxy instance, but clicking '2', '3', '4' or 'Show All" does take a second or more to display the response. Can you provide more information about the environment you have or what you are doing to reproduce this?

Thanks

Greg Von Kuster

On Feb 22, 2012, at 4:02 PM, David Hoover wrote:

> When I click on Admin->'Search and browse tool sheds'->'Galaxy main tool shed', it shows the first page of Valid repositories. However, clicking '2', '3', '4', or 'Show All' has no effect. I can only display the first page of repositories.
>
> However, if I search for valid tools using the menu under 'Galaxy main tool shed', I can get to any of the repositories listed at the Galaxy main toolshed.
>
> Is this a bug or a feature?
>
> David Hoover
> Helix Systems Staff
> ___________________________________________________________
> 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/

------------------------------

Message: 11
Date: Wed, 22 Feb 2012 22:07:59 +0100
From: Vipin TS <vipin.ts@gmail.com>
To: Galaxy Dev <galaxy-dev@bx.psu.edu>
Cc: Liusong Yang <liusongyang2009@gmail.com>
Subject: Re: [galaxy-dev] R scripts for DESeq
Message-ID:
<CAPipdU_3s5MgADC6oGfpNK3QcVuD6kM6bz-y1up_z9V1aQNiRg@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

We have the recent release version of DESeq at our Galaxy instance,

http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq

I will add the Galaxy wrapper for DESeq in community tool shed in few days.

regards,
--Vipin

Hi Lisa,
>
> I am going to send your question over to the galaxy-dev@bx.psu.edumailing list so that the development community can offer feedback.
> http://wiki.g2.bx.psu.edu/**Support#Starting_a_technical.**
> 2C_local.2BAC8-cloud_instance.**2C_or_development_thread<http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-cloud_instance.2C_or_development_thread>
>
> Th galaxy-user list is primarily for tool/data usage on the Galaxy public
> server.
> http://wiki.g2.bx.psu.edu/**Mailing%20Lists<http://wiki.g2.bx.psu.edu/Mailing%20Lists>
>
> Thanks,
>
> Jen
> Galaxy team
>
>
> -------- Original Message --------
> Subject: [galaxy-user] R scripts for DESeq
> Date: Tue, 21 Feb 2012 23:25:35 -0500
> From: Liusong Yang <liusongyang2009@gmail.com>
> To: galaxy-user@lists.bx.psu.edu
>
> Hello,
>
> I am planning to put DESeq into galaxy. I am a newcomer for both
> Galaxy and R. I have already read all of the related discussion in
> this group. I also noticed that there are r_wrapper.sh and DESeq.xml
> added into galaxy recently under the path of tools.
>
> These lines are from r_wrapper.sh.
>
> ### Run R providing the R script in $1 as standard input and passing
> ### the remaining arguments on the command line
>
>
> I guess this means we need to give the DESeq R script to the wrapper
> as standard input. My question is where or what is the DESeq R
> scripts? I installed R and DESeq package, but I can not fund anything
> like DESeq.R or something similar? I feel so confusing now. Any
> comments or suggestions would be absolutely appreciated!
>
> Thanks
>
> Lisa
> ______________________________**_____________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/**listinfo/galaxy-dev<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/
> ______________________________**_____________________________
> 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/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120222/2e863488/attachment-0001.html>

------------------------------

Message: 12
Date: Wed, 22 Feb 2012 16:18:00 -0500
From: David Hoover <hooverdm@helix.nih.gov>
To: Greg Von Kuster <greg@bx.psu.edu>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] limited tool shed browse
Message-ID: <BC510521-5384-47AA-B3CC-4443D9EC8556@helix.nih.gov>
Content-Type: text/plain; charset="us-ascii"

It's a local install, hg summary gives 6621:26920e20157f. I'm using MySQL as a backend database and have the following options set to non-default:

port = 8081
host = 0.0.0.0
tool_config_file = tool_conf.xml,shed_tool_conf.xml
install_tool_config_file = shed_tool_conf.xml
brand = Galaxy1
use_interactive = False
enable_whoosh_library_search = True
use_remote_user = True
allow_user_deletion = True
allow_user_impersonation = True
allow_user_dataset_purge = True
new_user_dataset_access_role_default_private = True
enable_quotas = True
retry_job_output_collection = 10
output_size_limit = 10737418240
start_job_runners = drmaa

On Feb 22, 2012, at 4:07 PM, Greg Von Kuster wrote:

> Hi David,
>
> I cannot reproduce this behavior from my local Galaxy instance, but clicking '2', '3', '4' or 'Show All" does take a second or more to display the response. Can you provide more information about the environment you have or what you are doing to reproduce this?
>
> Thanks
>
> Greg Von Kuster
>
> On Feb 22, 2012, at 4:02 PM, David Hoover wrote:
>
>> When I click on Admin->'Search and browse tool sheds'->'Galaxy main tool shed', it shows the first page of Valid repositories. However, clicking '2', '3', '4', or 'Show All' has no effect. I can only display the first page of repositories.
>>
>> However, if I search for valid tools using the menu under 'Galaxy main tool shed', I can get to any of the repositories listed at the Galaxy main toolshed.
>>
>> Is this a bug or a feature?
>>
>> David Hoover
>> Helix Systems Staff
>> ___________________________________________________________
>> 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/

------------------------------

Message: 13
Date: Wed, 22 Feb 2012 16:35:44 -0500
From: Greg Von Kuster <greg@bx.psu.edu>
To: David Hoover <hooverdm@helix.nih.gov>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] limited tool shed browse
Message-ID: <1E5022B4-690D-42C1-B6C0-6A150C8A0E79@bx.psu.edu>
Content-Type: text/plain; charset=us-ascii

What browser / version are you using?

On Feb 22, 2012, at 4:18 PM, David Hoover wrote:

> It's a local install, hg summary gives 6621:26920e20157f. I'm using MySQL as a backend database and have the following options set to non-default:
>
> port = 8081
> host = 0.0.0.0
> tool_config_file = tool_conf.xml,shed_tool_conf.xml
> install_tool_config_file = shed_tool_conf.xml
> brand = Galaxy1
> use_interactive = False
> enable_whoosh_library_search = True
> use_remote_user = True
> allow_user_deletion = True
> allow_user_impersonation = True
> allow_user_dataset_purge = True
> new_user_dataset_access_role_default_private = True
> enable_quotas = True
> retry_job_output_collection = 10
> output_size_limit = 10737418240
> start_job_runners = drmaa
>
> On Feb 22, 2012, at 4:07 PM, Greg Von Kuster wrote:
>
>> Hi David,
>>
>> I cannot reproduce this behavior from my local Galaxy instance, but clicking '2', '3', '4' or 'Show All" does take a second or more to display the response. Can you provide more information about the environment you have or what you are doing to reproduce this?
>>
>> Thanks
>>
>> Greg Von Kuster
>>
>> On Feb 22, 2012, at 4:02 PM, David Hoover wrote:
>>
>>> When I click on Admin->'Search and browse tool sheds'->'Galaxy main tool shed', it shows the first page of Valid repositories. However, clicking '2', '3', '4', or 'Show All' has no effect. I can only display the first page of repositories.
>>>
>>> However, if I search for valid tools using the menu under 'Galaxy main tool shed', I can get to any of the repositories listed at the Galaxy main toolshed.
>>>
>>> Is this a bug or a feature?
>>>
>>> David Hoover
>>> Helix Systems Staff
>>> ___________________________________________________________
>>> 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/
>
>

------------------------------

Message: 14
Date: Wed, 22 Feb 2012 15:47:42 -0800
From: Jennifer Jackson <jen@bx.psu.edu>
To: Sarah Diehl <diehl@immunbio.mpg.de>
Cc: "'galaxy-dev@lists.bx.psu.edu'" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] How to learn about new tools in the official
Tool Shed
Message-ID: <4F457E9E.5030200@bx.psu.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Sarah,

Bjoern is correct. A few other choices are:

We send out a tweet when new tools are added. This isn't automatic, or
necessarily for all tools, but something we plan on continuing. If
interested, you could follow us on twitter or track the Twitter wiki:
http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter

The "getgalaxy" search will find items in the Tool Shed, as well as
other Galaxy areas of developer interest (like the galaxy-dev list
threads):
http://wiki.g2.bx.psu.edu/News/Custom%20Galaxy%20Search

Best,

Jen
Galaxy team

On 2/20/12 1:01 AM, Sarah Diehl wrote:
> Hello,
>
> one quick question: is there a way to get news about new tools in the
> Tool Shed?
>
> I saw that I can subscribe to get news about already existing tools, but
> how about newly created ones? I would also be fine with some
> subscription to any changes in the Tool Shed in general.
>
> 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/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

------------------------------

Message: 15
Date: Wed, 22 Feb 2012 20:50:09 -0500
From: Liusong Yang <liusongyang2009@gmail.com>
To: Vipin TS <vipin.ts@gmail.com>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] R scripts for DESeq
Message-ID:
<CABWwarxYOhFPTQZ2t1CbJYyawEBU71YZCD_Bf80JHgErnU8S6Q@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Vipin,
That is a wonderful news and I am eager to see it in tool shed. I am
going to check tool shed frequently these days to get it asap.

Thanks
Lisa

On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS <vipin.ts@gmail.com> wrote:
> Hi,
>
> We have the recent release version of DESeq at our Galaxy instance,
>
> http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
>
> I will add the Galaxy wrapper for DESeq in community tool shed in few days.
>
> regards,
> --Vipin
>
>> Hi Lisa,
>>
>> I am going to send your question over to the galaxy-dev@bx.psu.edu mailing
>> list so that the development community can offer feedback.
>>
>> http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-cloud_instance.2C_or_development_thread
>>
>> Th galaxy-user list is primarily for tool/data usage on the Galaxy public
>> server.
>> http://wiki.g2.bx.psu.edu/Mailing%20Lists
>>
>> Thanks,
>>
>> Jen
>> Galaxy team
>>
>>
>> -------- Original Message --------
>> Subject: [galaxy-user] R scripts for DESeq
>> Date: Tue, 21 Feb 2012 23:25:35 -0500
>> From: Liusong Yang <liusongyang2009@gmail.com>
>> To: galaxy-user@lists.bx.psu.edu
>>
>> Hello,
>>
>> I am planning to put DESeq into galaxy. I am a newcomer for both
>> Galaxy and R. I have already read all of the related discussion in
>> this group. I also noticed that there are r_wrapper.sh and DESeq.xml
>> added into galaxy recently under the path of tools.
>>
>> These lines are from r_wrapper.sh.
>>
>> ### Run R providing the R script in $1 as standard input and passing
>> ### the remaining arguments on the command line
>>
>>
>> I guess this means we need to give the DESeq R script to the wrapper
>> as standard input. My question is where or what is the DESeq R
>> scripts? I installed R and DESeq package, but I can not fund anything
>> like DESeq.R or something similar? I feel so confusing now. Any
>> comments or suggestions would be absolutely appreciated!
>>
>> Thanks
>>
>> Lisa
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org. ?Please keep all replies on the list by
>> using "reply all" in your mail client. ?For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>> ?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/
>> ___________________________________________________________
>>
>> 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/
>
>

------------------------------

Message: 16
Date: Wed, 22 Feb 2012 21:27:27 -0500
From: Greg Von Kuster <greg@bx.psu.edu>
To: Liusong Yang <liusongyang2009@gmail.com>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] R scripts for DESeq
Message-ID: <DD093EB3-AF40-4ACB-81AD-79B0BB0D2FC4@bx.psu.edu>
Content-Type: text/plain; charset="us-ascii"

Lisa,

In case you aren't aware, you can set your user preferences for your account in the tool shed to receive an email message when a new repository's first upload occurs. This would keep you from having to check the tool shed. Go to User -> Preferences -> Manage your email alerts and you'll see the following setting.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: email_alert.tiff
Type: image/tiff
Size: 26606 bytes
Desc: not available
URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120222/77ae1e62/attachment-0001.tiff>
-------------- next part --------------

On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote:

> Hi Vipin,
> That is a wonderful news and I am eager to see it in tool shed. I am
> going to check tool shed frequently these days to get it asap.
>
> Thanks
> Lisa
>
> On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS <vipin.ts@gmail.com> wrote:
>> Hi,
>>
>> We have the recent release version of DESeq at our Galaxy instance,
>>
>> http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
>>
>> I will add the Galaxy wrapper for DESeq in community tool shed in few days.
>>
>> regards,
>> --Vipin
>>
>>> Hi Lisa,
>>>
>>> I am going to send your question over to the galaxy-dev@bx.psu.edu mailing
>>> list so that the development community can offer feedback.
>>>
>>> http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-cloud_instance.2C_or_development_thread
>>>
>>> Th galaxy-user list is primarily for tool/data usage on the Galaxy public
>>> server.
>>> http://wiki.g2.bx.psu.edu/Mailing%20Lists
>>>
>>> Thanks,
>>>
>>> Jen
>>> Galaxy team
>>>
>>>
>>> -------- Original Message --------
>>> Subject: [galaxy-user] R scripts for DESeq
>>> Date: Tue, 21 Feb 2012 23:25:35 -0500
>>> From: Liusong Yang <liusongyang2009@gmail.com>
>>> To: galaxy-user@lists.bx.psu.edu
>>>
>>> Hello,
>>>
>>> I am planning to put DESeq into galaxy. I am a newcomer for both
>>> Galaxy and R. I have already read all of the related discussion in
>>> this group. I also noticed that there are r_wrapper.sh and DESeq.xml
>>> added into galaxy recently under the path of tools.
>>>
>>> These lines are from r_wrapper.sh.
>>>
>>> ### Run R providing the R script in $1 as standard input and passing
>>> ### the remaining arguments on the command line
>>>
>>>
>>> I guess this means we need to give the DESeq R script to the wrapper
>>> as standard input. My question is where or what is the DESeq R
>>> scripts? I installed R and DESeq package, but I can not fund anything
>>> like DESeq.R or something similar? I feel so confusing now. Any
>>> comments or suggestions would be absolutely appreciated!
>>>
>>> Thanks
>>>
>>> Lisa
>>> ___________________________________________________________
>>> The Galaxy User list should be used for the discussion of
>>> Galaxy analysis and other features on the public server
>>> at usegalaxy.org. Please keep all replies on the list by
>>> using "reply all" in your mail client. For discussion of
>>> local Galaxy instances and the Galaxy source code, please
>>> use the Galaxy Development list:
>>>
>>> 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/
>>> ___________________________________________________________
>>>
>>> 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/
>

------------------------------

Message: 17
Date: Thu, 23 Feb 2012 08:16:06 +0000
From: "Bossers, Alex" <Alex.Bossers@wur.nl>
To: "'Jorrit Boekel'" <jorrit.boekel@scilifelab.se>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] uploads stuck in history
Message-ID: <FE8945BE2DE3F34795261679DC2F333DF713@SCOMP0934.wurnet.nl>
Content-Type: text/plain; charset="us-ascii"

I confirm the same strange behaviour since some of the last updates on the central version. We are at the latest now.
It is also with medium (10Mb+ tarballs) AND large files! Furthermore its seems to be in FireFox only.... They upload fine using IE8 or 9. Didn't test other browsers though.

Annoying it is indeed.

Alex

-----Oorspronkelijk bericht-----
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Jorrit Boekel
Verzonden: woensdag 22 februari 2012 10:15
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] uploads stuck in history

Dear list,

I have stumbled on some strange behaviour when uploading files to galaxy via the upload.py tool. At times, the upload seems to be stalled in history and is never actually performed, followed by a seemingly infinite history update (see log below). My system is Ubuntu 11.10 and runs Python 2.7.2. I find the behaviour in both my own modified galaxy install (based on galaxy-dist), and in a fresh clone from galaxy-central.

I have tried to upload different files, and all seem to sometimes trigger the behaviour, but not all the time. A restart of galaxy sometimes sorts things out. Common for the debug messages is that it seems there is never a job id generated as in "galaxy.tools.actions.upload_common INFO 2012-02-22 10:06:36,186 tool
upload1 created job id 2".

Has anyone seen similar things or can it be a problem with my system?

cheers,
jorrit

--------------Debug messa:

galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request returned None from get_history(): http://localhost:8080/
127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST /root/user_get_usage HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /root/user_get_usage HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:23 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:27 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:31 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:35 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:39 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:43 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:47 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"

___________________________________________________________
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/

------------------------------

Message: 18
Date: Thu, 23 Feb 2012 09:01:56 +0000
From: Christian Cole <C.Cole@dundee.ac.uk>
To: Greg Von Kuster <greg@bx.psu.edu>, Liusong Yang
<liusongyang2009@gmail.com>
Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>
Subject: Re: [galaxy-dev] R scripts for DESeq
Message-ID: <CB6BAEBF.F515%c.cole@dundee.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Which version of DESeq does this tool use?

Note that there are significant differences between DESeq 1.4 (the version
described in the paper) and 1.6.x (current release). The differences are
both in functionality and results.
Regards,

Chris

On 23/02/2012 02:27, "Greg Von Kuster" <greg@bx.psu.edu> wrote:

>Lisa,
>
>In case you aren't aware, you can set your user preferences for your
>account in the tool shed to receive an email message when a new
>repository's first upload occurs. This would keep you from having to
>check the tool shed. Go to User -> Preferences -> Manage
> your email alerts and you'll see the following setting.
>
>
>
>
>
>
>
>On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote:
>
>> Hi Vipin,
>> That is a wonderful news and I am eager to see it in tool shed. I am
>> going to check tool shed frequently these days to get it asap.
>>
>> Thanks
>> Lisa
>>
>> On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS <vipin.ts@gmail.com> wrote:
>>> Hi,
>>>
>>> We have the recent release version of DESeq at our Galaxy instance,
>>>
>>> http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
>>>
>>> I will add the Galaxy wrapper for DESeq in community tool shed in few
>>>days.
>>>
>>> regards,
>>> --Vipin
>>>
>>>> Hi Lisa,
>>>>
>>>> I am going to send your question over to the galaxy-dev@bx.psu.edu
>>>>mailing
>>>> list so that the development community can offer feedback.
>>>>
>>>>
>http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou
>d_instance.2C_or_development_thread
><http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo
>ud_instance.2C_or_development_thread>
>>>>
>>>> Th galaxy-user list is primarily for tool/data usage on the Galaxy
>>>>public
>>>> server.
>>>> http://wiki.g2.bx.psu.edu/Mailing%20Lists
>>>>
>>>> Thanks,
>>>>
>>>> Jen
>>>> Galaxy team
>>>>
>>>>
>>>> -------- Original Message --------
>>>> Subject: [galaxy-user] R scripts for DESeq
>>>> Date: Tue, 21 Feb 2012 23:25:35 -0500
>>>> From: Liusong Yang <liusongyang2009@gmail.com>
>>>> To: galaxy-user@lists.bx.psu.edu
>>>>
>>>> Hello,
>>>>
>>>> I am planning to put DESeq into galaxy. I am a newcomer for both
>>>> Galaxy and R. I have already read all of the related discussion in
>>>> this group. I also noticed that there are r_wrapper.sh and DESeq.xml
>>>> added into galaxy recently under the path of tools.
>>>>
>>>> These lines are from r_wrapper.sh.
>>>>
>>>> ### Run R providing the R script in $1 as standard input and passing
>>>> ### the remaining arguments on the command line
>>>>
>>>>
>>>> I guess this means we need to give the DESeq R script to the wrapper
>>>> as standard input. My question is where or what is the DESeq R
>>>> scripts? I installed R and DESeq package, but I can not fund anything
>>>> like DESeq.R or something similar? I feel so confusing now. Any
>>>> comments or suggestions would be absolutely appreciated!
>>>>
>>>> Thanks
>>>>
>>>> Lisa
>>>> ___________________________________________________________
>>>> The Galaxy User list should be used for the discussion of
>>>> Galaxy analysis and other features on the public server
>>>> at usegalaxy.org. Please keep all replies on the list by
>>>> using "reply all" in your mail client. For discussion of
>>>> local Galaxy instances and the Galaxy source code, please
>>>> use the Galaxy Development list:
>>>>
>>>> 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/
>>>> ___________________________________________________________
>>>>
>>>> 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/
>

The University of Dundee is a registered Scottish Charity, No: SC015096

------------------------------

Message: 19
Date: Thu, 23 Feb 2012 10:46:02 +0100
From: Vipin TS <vipin.ts@gmail.com>
To: Christian Cole <C.Cole@dundee.ac.uk>
Cc: Greg Von Kuster <greg@bx.psu.edu>, Galaxy Dev
<galaxy-dev@bx.psu.edu>, Liusong Yang <liusongyang2009@gmail.com>
Subject: Re: [galaxy-dev] R scripts for DESeq
Message-ID:
<CAPipdU_wYU6b3OJVo5SWp6sNVbKHQbkenEW32TA1erTKYDJr9w@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Chris,

We are running DESEQ_VERSION 1.6.0 at our instance
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq

thanks,
--Vipin T S

Which version of DESeq does this tool use?
>
> Note that there are significant differences between DESeq 1.4 (the version
> described in the paper) and 1.6.x (current release). The differences are
> both in functionality and results.
> Regards,
>
>
> Chris
>
> On 23/02/2012 02:27, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
>
> >Lisa,
> >
> >In case you aren't aware, you can set your user preferences for your
> >account in the tool shed to receive an email message when a new
> >repository's first upload occurs. This would keep you from having to
> >check the tool shed. Go to User -> Preferences -> Manage
> > your email alerts and you'll see the following setting.
> >
> >
> >
> >
> >
> >
> >
> >On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote:
> >
> >> Hi Vipin,
> >> That is a wonderful news and I am eager to see it in tool shed. I am
> >> going to check tool shed frequently these days to get it asap.
> >>
> >> Thanks
> >> Lisa
> >>
> >> On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS <vipin.ts@gmail.com> wrote:
> >>> Hi,
> >>>
> >>> We have the recent release version of DESeq at our Galaxy instance,
> >>>
> >>> http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
> >>>
> >>> I will add the Galaxy wrapper for DESeq in community tool shed in few
> >>>days.
> >>>
> >>> regards,
> >>> --Vipin
> >>>
> >>>> Hi Lisa,
> >>>>
> >>>> I am going to send your question over to the galaxy-dev@bx.psu.edu
> >>>>mailing
> >>>> list so that the development community can offer feedback.
> >>>>
> >>>>
> >
> http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou
> >d_instance.2C_or_development_thread
> ><
> http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo
> >ud_instance.2C_or_development_thread>
> >>>>
> >>>> Th galaxy-user list is primarily for tool/data usage on the Galaxy
> >>>>public
> >>>> server.
> >>>> http://wiki.g2.bx.psu.edu/Mailing%20Lists
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Jen
> >>>> Galaxy team
> >>>>
> >>>>
> >>>> -------- Original Message --------
> >>>> Subject: [galaxy-user] R scripts for DESeq
> >>>> Date: Tue, 21 Feb 2012 23:25:35 -0500
> >>>> From: Liusong Yang <liusongyang2009@gmail.com>
> >>>> To: galaxy-user@lists.bx.psu.edu
> >>>>
> >>>> Hello,
> >>>>
> >>>> I am planning to put DESeq into galaxy. I am a newcomer for both
> >>>> Galaxy and R. I have already read all of the related discussion in
> >>>> this group. I also noticed that there are r_wrapper.sh and DESeq.xml
> >>>> added into galaxy recently under the path of tools.
> >>>>
> >>>> These lines are from r_wrapper.sh.
> >>>>
> >>>> ### Run R providing the R script in $1 as standard input and passing
> >>>> ### the remaining arguments on the command line
> >>>>
> >>>>
> >>>> I guess this means we need to give the DESeq R script to the wrapper
> >>>> as standard input. My question is where or what is the DESeq R
> >>>> scripts? I installed R and DESeq package, but I can not fund anything
> >>>> like DESeq.R or something similar? I feel so confusing now. Any
> >>>> comments or suggestions would be absolutely appreciated!
> >>>>
> >>>> Thanks
> >>>>
> >>>> Lisa
> >>>> ___________________________________________________________
> >>>> The Galaxy User list should be used for the discussion of
> >>>> Galaxy analysis and other features on the public server
> >>>> at usegalaxy.org. Please keep all replies on the list by
> >>>> using "reply all" in your mail client. For discussion of
> >>>> local Galaxy instances and the Galaxy source code, please
> >>>> use the Galaxy Development list:
> >>>>
> >>>> 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/
> >>>> ___________________________________________________________
> >>>>
> >>>> 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/
> >
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> ___________________________________________________________
> 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/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120223/55216fdb/attachment-0001.html>

------------------------------

Message: 20
Date: Thu, 23 Feb 2012 13:48:25 +0000
From: Peter Cock <p.j.a.cock@googlemail.com>
To: dannonbaker@me.com
Cc: "<galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Splitting large jobs over multiple
nodes/CPUs?
Message-ID:
<CAKVJ-_7ObF5L-xuDJuPJFF9ASxNHHM+US6fcvz1JXkoXJqQk4w@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Wed, Feb 22, 2012 at 7:07 PM, <dannonbaker@me.com> wrote:
> Awesome, I'll take a look. ?And, if you're able to pull it together easily
> enough, clean branches are always nice.
>
> -Dannon

It is all on one new branch, but this covers FASTA splitting (ready),
splitting in the BLAST+ wrapper (ready bar merging datatypes),
XML merging (may need more work). It has also occurred to me
I may need to implement HTML merging (or even remove this as
a BLAST output option - do people use it?).

https://bitbucket.org/peterjc/galaxy-central/src/split_blast

All the commits should be self contained allowing the FASTA
splitting bits to be transplanted/cherry-picked. If you want I'll do
that on a new branch focused on FASTA splitting only.

But before I do, I'd appreciate any initial comments you might
have from a first inspection.

Thanks,

Peter

------------------------------

_______________________________________________
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev

End of galaxy-dev Digest, Vol 68, Issue 31
******************************************