Re: [galaxy-dev] correctly installing to toolshed

[Xianrong Wong]

Thank you!

On Thu, Feb 25, 2016 at 7:50 PM, Karen Reddy  wrote:

> Thanks!
>
> Sent from Nine 
>
> *From:* Gildas Le Corguillé 
> *Sent:* Feb 25, 2016 3:17 PM
> *To:* Karen Reddy
> *Cc:* Xianrong; Björn Grüning; Xianrong Wong; galaxy-...@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] correctly installing to toolshed
>
> Hi all,
>
> You will found in attachment the modification, I proposed in my first
> email.
>
> As I said when your script is near your xml, you just need to use the
> interpreter attribute in 
>
>
>
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Re: [galaxy-dev] AssertionError: there is no script for 130 version

[Dannon Baker]

Hey Bill,

The only time I've seen this is when switching from (for example) tip of
the 'dev' brach of Galaxy over to 16.01, 15.10, or some other stable
release.

Basically, sqlalchemy_migrate sees the 0130_change_pref_datatype.pyc (or
some other one) and thinks a version should exist.

The easiest fix for this is something like:  `find . -name "*.pyc"
-delete`, executed from your galaxy root directory.

-Dannon


On Thu, Feb 25, 2016 at 3:50 PM, William Ge  wrote:

> Hi, all,
>
>
>
> I  am new to Galaxy. The following error was encountered when I tried to
> run Galaxy after getting PostgreSQL up:
>
>
>
> File
> "/home/galaxy/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg/migrate/versioning/version.py",
> line 204, in script
>
> "There is no script for %d version" % self.version
>
> AssertionError: There is no script for 130 version
>
>
>
> I searched the lists and forums, but have not found any message. Anyone
> can give some hits?
>
>
>
> I’m running this on CentOS 6.7, virtual environment, python2.6, PostgresQL
> 8.4.20.
>
>
>
> Thanks in advance!
>
>
>
> Bill
>
>
>
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[galaxy-dev] AssertionError: there is no script for 130 version

[William Ge]

Hi, all,

I  am new to Galaxy. The following error was encountered when I tried to run 
Galaxy after getting PostgreSQL up:

File 
"/home/galaxy/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg/migrate/versioning/version.py",
 line 204, in script
"There is no script for %d version" % self.version
AssertionError: There is no script for 130 version

I searched the lists and forums, but have not found any message. Anyone can 
give some hits?

I'm running this on CentOS 6.7, virtual environment, python2.6, PostgresQL 
8.4.20.

Thanks in advance!

Bill

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[galaxy-dev] Lost prostgresql database

[Raphenya, Amogelang]

Hi All,


Our server hard drive failed and we lost the database which was running galaxy instance.


But we did NOT loose all the data i.e all the files are there under the /galaxy-dist
directory.


Is there a way to reconstruct the database using the data itself.


Please help.













Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya














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Re: [galaxy-dev] Query

[Daniel Blankenberg]

Hi Chang-Hyuk,


If you click on the bug icon for your error'd dataset you should be able to get 
the full traceback.


Thanks for using Galaxy,


Dan



> Dear Sir,
> 
> that is all of error message.
> I attached the file to be tried.
> 
> best regards,
> Chang-Hyuk Yoo.
> 
> 2016-02-25 오전 4:13에 Vipin TS 이(가) 쓴 글:
>> Hi Chang-Hyuk, 
>> 
>> Looks like the traceback truncated, Could you please pass me the complete 
>> error message from the job run, then I will have a look.   
>> 
>> Vipin | Rätsch Lab
>> 
>> On Tue, Feb 23, 2016 at 11:04 PM, 유창혁  wrote:
>> Dear Sir,
>> 
>> I used your "Convert Format" from gff file of NCBI.
>> but I encounter the following message.
>> What can I do?
>> 
>> Best regards,
>> Chang-Hyuk Yoo.
>> Traceback (most recent call last):
>>   File 
>> "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/5c6f33e20fcc/fml_gff3togtf/gff_to_gtf.py",
>>  line 76, in 
>> printGTF(Transcriptdb) 
>>   File "/home/galaxy/shed_tools/toolshed.g2.
>> 
>> 
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Re: [galaxy-dev] Broken package_perl_5_18, was Re: JBrowse on dev branch: progress

[Peter van Heusden]

I knew there was an email that I forgot to send! Nicola Soranzo fixed this
with galaxy PR https://github.com/galaxyproject/galaxy/pull/1775 - sometime
in November last year Eric added whitespace to the perl package (and a
bunch of other things) that broke the download_file action, so Nicola's
patch strips whitespace. (The conversation about this happened on IRC and
the PR)

I tested the PR and it makes the perl install work (which makes the JBrowse
installl work, yay!).

Peter
On 25 Feb 2016 6:10 PM, "Peter Briggs" 
wrote:

> Hello Peter
>
> Re the failing install of 'package_perl_5_18', I've investigated further
> now and have submitted a patch which seems to fix the problem:
>
> https://github.com/galaxyproject/tools-iuc/pull/616
>
> Not sure if this is of any immediate help,
>
> Best wishes
>
> Peter
>
> On 22/02/16 09:43, Peter van Heusden wrote:
>
>> Ok, second attempt, perl install died with the same error, so I suspect
>> you're right about the cause. Eric?
>>
>> Peter
>>
>> On 22 February 2016 at 11:41, Peter van Heusden > > wrote:
>>
>> Thanks Peter
>>
>> I managed, on the second attempt, to get past the gnu coreutils
>> problem. Zipho noticed a weird lockup though: conftest that seemed
>> to be from the gnu coreutils install wanted to listen on port 4001,
>> which is the same port our uwsgi server listens on. The install has
>> now completed but I'll try and find time to go back and verify this.
>>
>> On the second attempt perl seems to be installing, so I'll see if it
>> completes or hits the error you're mentioning.
>>
>> Peter
>>
>> On 22 February 2016 at 11:34, Peter Briggs
>> > > wrote:
>>
>> Hi Peter
>>
>> I think that package_perl_5_18 in the tool shed is broken, I
>> came across the same error last week on both our production
>> instance and a local 'test' instance (both v15.10).
>>
>> My suspicion is that the following lines are to blame:
>>
>> ...
>>  >
>> sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b"
>> type="download_file">
>>
>> http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz
>>  
>>  tar xfvz
>> local-lib-1.008009.tar.gz
>> ...
>>
>> Looking at the Galaxy internals I believe that the
>> 'download_file' action automatically unpacks the archive and
>> cd's into the resulting directory, hence the failure for the
>> subsequent 'tar xfvz ...' command. But I haven't had the time
>> yet to verify this or create a patch to see if the removal of
>> this line addresses the problem.
>>
>> I don't think I've seen the problem with
>> 'package_gnu_coreutils_8_22' that you describe however so it may
>> be that my hypothesis is not correct.
>>
>> HTH
>>
>> Best wishes
>>
>> Peter
>>
>>
>> On 22/02/16 05:10, Peter van Heusden wrote:
>>
>> Hi there Eric and others
>>
>> I tried to install the JBrowse tool on a dev branch server
>> running on an
>> Ubuntu 14.04 VM.
>>
>> It got stuck at the package_gnu_coreutils_8_22 dependency
>> (revision
>> ac64dfe4b1fb) - this ended up in "Installing tool
>> dependencies" state.
>>
>> If I go look at the tool details it highlights errors
>> in package_perl_5_18 which in turn refers to errors in
>> gnu_coreutils
>> (just "Error" state) and then this more informative failure
>> for perl:
>>
>> "tar (child): local-lib-1.008009.tar.gz: Cannot open: No
>> such file or
>> directory
>> tar (child): Error is not recoverable: exiting now
>> tar: Child returned status 2
>> tar: Error is not recoverable: exiting now"
>>
>> I wonder if this is a sign of a download error?
>>
>> Digging a bit more I find the error "Shutting down process
>> id 21094
>> because it generated no output for the defined timeout
>> period of 3600.0
>> seconds." for gnu_coreutils.
>>
>> I'm trying to do a reinstall of the gnu_coreutils and perl
>> packages to
>> see if I can get further.
>>
>> Peter
>>
>>
>> ___
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>>
>> To search Galaxy 

[galaxy-dev] Broken package_perl_5_18, was Re: JBrowse on dev branch: progress

[Peter Briggs]

Hello Peter

Re the failing install of 'package_perl_5_18', I've investigated further 
now and have submitted a patch which seems to fix the problem:


https://github.com/galaxyproject/tools-iuc/pull/616

Not sure if this is of any immediate help,

Best wishes

Peter

On 22/02/16 09:43, Peter van Heusden wrote:

Ok, second attempt, perl install died with the same error, so I suspect
you're right about the cause. Eric?

Peter

On 22 February 2016 at 11:41, Peter van Heusden > wrote:

Thanks Peter

I managed, on the second attempt, to get past the gnu coreutils
problem. Zipho noticed a weird lockup though: conftest that seemed
to be from the gnu coreutils install wanted to listen on port 4001,
which is the same port our uwsgi server listens on. The install has
now completed but I'll try and find time to go back and verify this.

On the second attempt perl seems to be installing, so I'll see if it
completes or hits the error you're mentioning.

Peter

On 22 February 2016 at 11:34, Peter Briggs
> wrote:

Hi Peter

I think that package_perl_5_18 in the tool shed is broken, I
came across the same error last week on both our production
instance and a local 'test' instance (both v15.10).

My suspicion is that the following lines are to blame:

...
 
http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz
 
 tar xfvz
local-lib-1.008009.tar.gz
...

Looking at the Galaxy internals I believe that the
'download_file' action automatically unpacks the archive and
cd's into the resulting directory, hence the failure for the
subsequent 'tar xfvz ...' command. But I haven't had the time
yet to verify this or create a patch to see if the removal of
this line addresses the problem.

I don't think I've seen the problem with
'package_gnu_coreutils_8_22' that you describe however so it may
be that my hypothesis is not correct.

HTH

Best wishes

Peter


On 22/02/16 05:10, Peter van Heusden wrote:

Hi there Eric and others

I tried to install the JBrowse tool on a dev branch server
running on an
Ubuntu 14.04 VM.

It got stuck at the package_gnu_coreutils_8_22 dependency
(revision
ac64dfe4b1fb) - this ended up in "Installing tool
dependencies" state.

If I go look at the tool details it highlights errors
in package_perl_5_18 which in turn refers to errors in
gnu_coreutils
(just "Error" state) and then this more informative failure
for perl:

"tar (child): local-lib-1.008009.tar.gz: Cannot open: No
such file or
directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now"

I wonder if this is a sign of a download error?

Digging a bit more I find the error "Shutting down process
id 21094
because it generated no output for the defined timeout
period of 3600.0
seconds." for gnu_coreutils.

I'm trying to do a reinstall of the gnu_coreutils and perl
packages to
see if I can get further.

Peter


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--
Peter Briggs peter.bri...@manchester.ac.uk

Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482





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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] Galaxy 16.01 Release

[Makis Ladoukakis]

Thanks a lot Nate! You are right!

yum install mariadb-devel

did the trick.

Cheers,
Makis

From: n...@bx.psu.edu
Date: Thu, 25 Feb 2016 10:12:51 -0500
Subject: Re: [galaxy-dev] Galaxy 16.01 Release
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

On Thu, Feb 25, 2016 at 2:49 AM, Makis Ladoukakis  
wrote:



Just upgraded from the last version and after I run the run.sh script I get the 
following error:

mysql_config: command not found
Traceback (most recent call last):
  File "", line 1, in 
  File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in 
metadata, options = get_config()
  File "setup_posix.py", line 43, in get_config
libs = mysql_config("libs_r")
  File "setup_posix.py", line 25, in mysql_config
raise EnvironmentError("%s not found" % (mysql_config.path,))
EnvironmentError: mysql_config not found



Any idea why? 

I am running on CentOS 7.1.1503  with MariaDB installed.

Hi Makis,
Please make sure that you have the -devel package for MariaDB installed. 
MySQL_Python is looking for the `mysql_config` command to be able to build, but 
it's not present on your system.
--nate 

Kind regards,
Makis

From: n...@bx.psu.edu
Date: Wed, 24 Feb 2016 16:56:19 -0500
To: galaxy-annou...@lists.galaxyproject.org; galaxy-dev@lists.galaxyproject.org
CC: galaxy-committ...@lists.galaxyproject.org
Subject: [galaxy-dev] Galaxy 16.01 Release

The Galaxy Committers team is pleased to announce the January 2016 (v16.01) 
release of Galaxy. Galaxy administrators should also be aware of the security 
announcements that I am posting simultaneously with this release announcement. 
The release notes follow.

From: https://docs.galaxyproject.org/en/master/releases/16.01_announce.html


January 2016 Galaxy Release (v 16.01)
Highlights
Interactive Tours
The interactive tours framework allows developers and deployers to build 
interactive tutorials for users superimposed on the actual Galaxy web front 
end. Unlike video tutorials, these will not become stale and are truly 
interactive (allowing users to actually navigate and interact with Galaxy). 
Galaxy 16.01 ships with two example tours and new ones can easily be added by 
creating a small YAML file describing the tour. Try the Galaxy UI tour on Main.
Wheels
Galaxy’s Python dependencies have traditionally been distributed as eggs using 
custom dependency management code to enable Galaxy to distribute binary 
dependencies (enabling quick downloads and minimal system requirements). With 
this release all of that infrastructure has been replaced with a modern Python 
infrastructure based on pip and wheels. Work done as part of this to enable 
binary dependencies on Linux has been included with the recently released pip 8.
Detailed documentation on these changes and their impact under a variety of 
Galaxy deployment scenarios can be found in the Galaxy Framework Dependencies 
section of the Admin documentation.
Nested Workflows
Workflows may now run other workflows as a single abstract step in the parent 
workflow. This allows for reusing or subworkflows in your analyses.
Github
New% git clone -b master https://github.com/galaxyproject/galaxy.gitUpdate to 
latest stable release% git checkout master && pull --ff-only origin 
masterUpdate to exact version% git checkout v16.01
BitBucket
Upgrade% hg pull% hg update latest_16.01
See our wiki for additional details regarding the source code locations.
Deprecation Notices
Barring a strong outcry from deployers, 16.01 will be the last release of 
Galaxy to support Python 2.6. For more information, see Galaxy Github Issue 
#1596.

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Re: [galaxy-dev] Collapse tool panel and history panel

[Marius van den Beek]

Hi Makis,

if you change the javascript in client/ ... you need to run grunt.
The instructions are in
https://github.com/galaxyproject/galaxy/blob/dev/client/README.md.

Cheers,
Marius

On 25 February 2016 at 10:57, Makis Ladoukakis 
wrote:

> Just an update/bump of the issue. With the new 16.01 version I made the
> changes in the /client/galaxy/scripts/apps/analysis.js
> b/client/galaxy/scripts/apps/analysis.js file but the none of the panels
> were collapsed even when i restarted my Galaxy instance.
>
> I don't really get the mechanics behind it. Seems like any changes i do
> either in the js files or the mako scripts never take effect in the actual
> instance. I even tried to delete everything in there leaving just a blank
> file to test my theory and after restart the Galaxy instance initializes
> with no errors at all.
>
> Any ideas?
> Makis
>
> --
> From: makis4e...@hotmail.com
> To: dannon.ba...@gmail.com
> Date: Mon, 22 Feb 2016 13:47:59 +0200
> CC: galaxy-...@lists.bx.psu.edu
>
> Subject: Re: [galaxy-dev] Collapse tool panel and history panel
>
> The git log ..origin/master command produced no output so I guess I have
> the latest release (15.10.1 maybe?). The git pull command confirmed that.
> Should I use a release from the dev branch?
>
> Kind regards,
> Makis
>
> --
> Date: Fri, 19 Feb 2016 08:39:35 -0500
> Subject: Re: [galaxy-dev] Collapse tool panel and history panel
> From: dannon.ba...@gmail.com
> To: makis4e...@hotmail.com
> CC: galaxy-...@lists.bx.psu.edu
>
> Sure, I can help.  Which version of Galaxy are you currently running?  I
> didn't check the history very well and the fix I suggested will work for
> the forthcoming 16.01 release (or current dev branch), but not 15.10.
>
>
> On Fri, Feb 19, 2016 at 8:32 AM, Makis Ladoukakis 
> wrote:
>
> Hello Dannon,
>
> Sorry for asking but can you help me out a little bit with that? I
> searched in my galaxy directory in order to add those two lines you mention
> in the link but there is no galaxy/scripts/apps/analysis.js file and
> neither any file containing the string 'analysisPage.right.historyView'.
>
> Any advice?
>
> Thank you,
> Makis
> --
> Date: Mon, 28 Dec 2015 14:30:02 -0500
> Subject: Re: [galaxy-dev] Collapse tool panel and history panel
> From: dannon.ba...@gmail.com
> To: makis4e...@hotmail.com
> CC: galaxy-...@lists.bx.psu.edu
>
>
> Hi Makis,
>
> We've restructured much of the client code fairly recently.  Something
> like this should work for you now:
>
> https://gist.github.com/dannon/bd470d9c70019b07cb8b
>
>
> Sorry for the slow response!
>
> -Dannon
>
>
> On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis 
> wrote:
>
> Shamelessly bumping my own question... Does anyone have any ideas about
> collapsing the history and tool panel?
>
> Thank you,
> Makis Ladoukakis
>
> --
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu
> Date: Wed, 16 Dec 2015 13:41:19 +0200
> Subject: [galaxy-dev] Collapse tool panel and history panel
>
>
> Hello,
>
> Does anyone know how to start my Galaxy instance with the history panel
> and tool panel collapsed by default?
>
> I used to do it by editing the galaxy/templates/base/base_panels.mako
> script and adding
>
> *lp.do_toggle();*
>
> and
>
>
>
> *rp.do_toggle();*inside the if sections of *%if self.has_left_panel: *and *%if
> self.has_right_panel: *respectively but with my new installed instance
> this doesn't seem to work anymore.
>
> Any ideas anyone?
>
> Thank you,
> Makis Ladoukakis
>
>
>
>
> ___ Please keep
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>
>
>
>
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Re: [galaxy-dev] Collapse tool panel and history panel

[Makis Ladoukakis]

Just an update/bump of the issue. With the new 16.01 version I made the changes 
in the /client/galaxy/scripts/apps/analysis.js 
b/client/galaxy/scripts/apps/analysis.js file but the none of the panels were 
collapsed even when i restarted my Galaxy instance.

I don't really get the mechanics behind it. Seems like any changes i do either 
in the js files or the mako scripts never take effect in the actual instance. I 
even tried to delete everything in there leaving just a blank file to test my 
theory and after restart the Galaxy instance initializes with no errors at all.

Any ideas?
Makis

From: makis4e...@hotmail.com
To: dannon.ba...@gmail.com
Date: Mon, 22 Feb 2016 13:47:59 +0200
CC: galaxy-...@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Collapse tool panel and history panel




The git log ..origin/master command produced no output so I guess I have the 
latest release (15.10.1 maybe?). The git pull command confirmed that. Should I 
use a release from the dev branch?

Kind regards,
Makis

Date: Fri, 19 Feb 2016 08:39:35 -0500
Subject: Re: [galaxy-dev] Collapse tool panel and history panel
From: dannon.ba...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu

Sure, I can help.  Which version of Galaxy are you currently running?  I didn't 
check the history very well and the fix I suggested will work for the 
forthcoming 16.01 release (or current dev branch), but not 15.10.

On Fri, Feb 19, 2016 at 8:32 AM, Makis Ladoukakis  
wrote:



Hello Dannon,

Sorry for asking but can you help me out a little bit with that? I searched in 
my galaxy directory in order to add those two lines you mention in the link but 
there is no galaxy/scripts/apps/analysis.js file and neither any file 
containing the string 'analysisPage.right.historyView'. 

Any advice?

Thank you,
Makis
Date: Mon, 28 Dec 2015 14:30:02 -0500
Subject: Re: [galaxy-dev] Collapse tool panel and history panel
From: dannon.ba...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu

Hi Makis,
We've restructured much of the client code fairly recently.  Something like 
this should work for you now:
https://gist.github.com/dannon/bd470d9c70019b07cb8b


Sorry for the slow response!
-Dannon

On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis  
wrote:



Shamelessly bumping my own question... Does anyone have any ideas about 
collapsing the history and tool panel?

Thank you,
Makis Ladoukakis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu
Date: Wed, 16 Dec 2015 13:41:19 +0200
Subject: [galaxy-dev] Collapse tool panel and history panel




Hello,

Does anyone know how to start my Galaxy instance with the history panel and 
tool panel collapsed by default?

I used to do it by editing the galaxy/templates/base/base_panels.mako script 
and adding

lp.do_toggle();

and 

rp.do_toggle();

inside the if sections of %if self.has_left_panel: and %if 
self.has_right_panel: respectively but with my new installed instance this 
doesn't seem to work anymore.

Any ideas anyone?

Thank you,
Makis Ladoukakis



  

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