Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Peter Cock]

On Wed, Aug 7, 2013 at 3:41 AM, Rodolfo Aramayo  wrote:
> On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock  wrote:
>>
>> Looks like your BOOST is too new for BLAST 2.2.26+ (which
>> just recently became a problem on the Galaxy Tool Shed testing
>> system as well).
>>
>> In the short term I'm hoping to update the Tool Shed repository
>> to use the NCBI provided pre-compiled binaries. I'm in discussion
>> with Galaxy's Dave Bouvier about how best to do that, perhaps
>> with some relatively new functionality added to Galaxy. Next,
>> updating the BLAST+ version (and the unit tests to match).
>>
>> I would suggest right now you manually install BLAST+ using
>> the NCBI provided binaries.
>>
>> Peter
>
> Boost is a funny thing
> Changes a lot
> A package compiled with one Boost version might fail to compile with a
> newer one. I have seen it a lot
> You either have to download Boost and link to the specific version you
> want before compiling your package or provide pre-compiled binaries
> The question I have is: How many Galaxy packages have Boos as a
> dependency for compilation? and if the answer is: a lot, then would it
> be smart for Galaxy to have a place where it can keep versions of
> these commonly-used libraries so that they can be linked by packages
> that need to be compiled 'in-situ' or would it be just more efficient
> to provide pre-compiled binaries?
> Something tells me that pre-compiled binaries might not take full
> advantage of the hardware they are and that compiling is better...
> So, should ToolShed installation require automatic download of a set
> of pre-defined commonly-used libraries?

That's probably possible via a Tool Shed dependency,
Bjoern has been working on this on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_boost_1_53

Now under a shared IUC account:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53

Peter
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[galaxy-dev] Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable)

[Rodolfo Aramayo]

Attempting to run oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz)
on Galaxy fd4113962c32+ (stable)
I get the following error:
#
error
An error occurred with this dataset: Traceback (most recent call
last): File 
"/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py",
line 120, in if __name__ == "__main__": __main
#
Traceback (most recent call last):
  File 
"/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py",
line 120, in 
if __name__ == "__main__": __main__()
  File 
"/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py",
line 69, in __main__
for line in open(transcript_path):
IOError: [Errno 2] No such file or directory: 'transcripts.fa'
#

The input file is part of my history and it is in fastqsanger format
I get the same error after converting fastqsanger to fasta format

Ideas?

Thanks

--Rodolfo
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[galaxy-dev] RFC: Implement 'cloudbiolinux_install' tool shed package install action.

[John Chilton]

I have implemented a cool idea Brad Chapman had the recent BOSC
Codefest. It would save me tons of effort related to maintaining
separate proteomics module definitions for the tool shed and
CloudBioLinux for Galaxy-P.

I thought I would throw this out there and see if anyone has any comments:

>From the pull request:

CloudBioLinux contains custom fabric install procedures for dozens of
bioinformatics packages and new ones are added all the time. It also
contains code used to automatically setup Galaxy env.sh files to
support multiple versions of given software. While it started off as a
way to configure a particular distribution of Linux, it now supports
many distributions and these custom install procedures in particular
are not tied to any particular varaint of Linux or even Linux itself.

This changeset adds the ability for Tool Shed tools to quickly and
easily leverage this wealth of Galaxy module ready software.

In particular it adds a new action type - 'cloudbiolinux_install'. I
have created the repository 'ngscbltest' in 'Next Gen Mappers' section
on the Test Tool Shed to demonstrate and test this functionality.

Here is an example from 'tool_dependencies.xml' in that repository:





  


Tophat 2.

...


When installed into a Galaxy instance, this example will cause the
version '2.0.8b' to be passed to the 'install_tophat2' function in
CloudBioLinux and configure it to install into the directory expected
by the Tool Shed client code. Additonally, CloudBioLinux will setup an
env.sh file for this installation. All of this will be installed as a
'tophat2' package.

In the above example,a particulr revision of CloudBioLinux was
specified for the sake of reproducibility. That attribute is optional
however and will default to 'master'. Likewise, reasonble defaults for
the attributes 'tool_name' and 'tool_version' can be inferred from
context. As a demonstration, the following package definition would
result in Tophat 1.3.3 being installed as the package 'tophat'.




  


Tophat 1.3.3.


The name of install method doesn't have to match the packge name, for
instance the install_cufflinks function in CloudBioLinux can be used
to install Cufflinks 1 or 2 as shown below:




  https://github.com/jmchilton/cloudbiolinux.git";
  tool_name="cufflinks" />


Cufflinks2.


This final example also demonstrates how to target a customized fork
of CloudBioLinux.

Implementation: On the Galaxy side of this equation, the
implementation is fairly straight forward. fabric_util.py has been
updated with a '__install_cloudbiolinux_tool' function which
implements this action entirely. This function clones clodubiolinux to
a temporary directory (optionally checking out a particular revision),
and uses the CloudBioLinux deployer functionality to configure a
local, no-ssh install of the specified software.

Requirements: The core framework for obtaining and running
CloudBioLinux requires only bash, wget, git, and
python-dev/python-devel. These are likely a subset of packages the IUC
has already agreed will need to be present. Individual install
procedures may have additonal OS level requirements, but the same
could be true of any Make file compiled with the existing Tool Shed
infrastructure. If particular modules are isolated as being useful, I
am happy to work with the tool developers to ensure the CloudBioLinux
install procedure can work with minimal prerequisites.

Thanks,
-John
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Rodolfo Aramayo]

On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock  wrote:
> On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo  wrote:
>> Dave,
>>
>> It did contain errors as reported by tailing the last part of the
>> INSTALLATION.log
>>
>> Thanks
>>
>> --Rodolfo
>
> Looks like your BOOST is too new for BLAST 2.2.26+ (which
> just recently became a problem on the Galaxy Tool Shed testing
> system as well).
>
> In the short term I'm hoping to update the Tool Shed repository
> to use the NCBI provided pre-compiled binaries. I'm in discussion
> with Galaxy's Dave Bouvier about how best to do that, perhaps
> with some relatively new functionality added to Galaxy. Next,
> updating the BLAST+ version (and the unit tests to match).
>
> I would suggest right now you manually install BLAST+ using
> the NCBI provided binaries.
>
> Peter

Boost is a funny thing
Changes a lot
A package compiled with one Boost version might fail to compile with a
newer one. I have seen it a lot
You either have to download Boost and link to the specific version you
want before compiling your package or provide pre-compiled binaries
The question I have is: How many Galaxy packages have Boos as a
dependency for compilation? and if the answer is: a lot, then would it
be smart for Galaxy to have a place where it can keep versions of
these commonly-used libraries so that they can be linked by packages
that need to be compiled 'in-situ' or would it be just more efficient
to provide pre-compiled binaries?
Something tells me that pre-compiled binaries might not take full
advantage of the hardware they are and that compiling is better...
So, should ToolShed installation require automatic download of a set
of pre-defined commonly-used libraries?


--Rodolfo
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Re: [galaxy-dev] Local installation: Questions about using rsync to retrieve a genome

[Gerald Bothe]

I'll leave the rsync question to the experts - worked for me, but I don't know 
why it worked for me (linux/ubuntu laptop, not networked) and not for you .
 
About the filenames: You can download a file listing to text.txt by
 
.../galaxy-dist$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes > text.txt
 
and then choose which one you want. File size warning: this is something like 
200 MB. Trying to download the much shorter list for phiX might be a quick way 
to check whether it works:
 
.../galaxy-dist$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX > 
phiXlist.txt

Gerald 


>
> From: Boaz Shaanan 
>To: "galaxy-dev@lists.bx.psu.edu"  
>Sent: Tuesday, August 6, 2013 4:25 PM
>Subject: [galaxy-dev] Local installation: Questions about using rsync to 
>retrieve a genome
>  
>
>
> 
>Hi, 
>
> 
>1) I'd like to fetch the genome of H. salinarum NRC-1 on my local 
>installation. Following your advice 
>(http://wiki.galaxyproject.org/Admin/Data%20Integration 
>I wanted to use rsync. To begin with I tried the example in the above url, 
>even though that's not the genome I'm interested in: 
>  
>
> rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . 
>  
>I didn't get any response. My questions are: 
>1) Is it because the ftp site was not on ? Or could it be a firewall problem? 
>Can the site be accessed in a different way that I can try? 
>2)Where can I find the file name where the H. salinarum NRC-1 genome resides 
>on the server? 
>
> 
> Thanks for your help. 
>
> 
>                                  Boaz 
>
> 
>Boaz Shaanan, Ph.D. 
>Dept. of Life Sciences  
>Ben-Gurion University of the Negev  
>Beer-Sheva 84105    
>Israel  
>    
>E-mail: bshaa...@bgu.ac.il
>Phone: 972-8-647-2220  Skype: boaz.shaanan  
>Fax:   972-8-647-2992 or 972-8-646-1710 
>  
>  
> 
>
>  
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>
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Re: [galaxy-dev] Running local galaxy installation while another httpd is operating on the same computer

[Nate Coraor]

On Aug 5, 2013, at 12:33 PM, Boaz Shaanan wrote:

> Hi,
> 
> I think I'm running into a problem of getting my local galaxy installation 
> server to start because another httpd server is currently running on the same 
> computer (see attached output of run.sh). Toward the end I notice that the 
> server starts with PID number but then runs into a socket conflict (probably 
> with the other server) and stops. Is there a way to get over this problem?
> 
>Thanks for your help.
> 
>  Boaz

Hi Boaz,

If you're starting on a port other than 80 and intend to just access that port 
directly or via a proxy server, you can change the port number at the top of 
universe_wsgi.ini.  If you're trying to start Galaxy on port 80, you'll have to 
decide which application you want to give that privilege to, since it can't be 
more than one.  However, a common and recommended solution to this problem is 
to run a proxy server on port 80.  Instructions on how to place Galaxy behind a 
proxy server are available at:

  http://usegalaxy.org/production

--nate

>  
>  
> Boaz Shaanan, Ph.D. 
> Dept. of Life Sciences  
> Ben-Gurion University of the Negev  
> Beer-Sheva 84105
> Israel  
> 
> E-mail: bshaa...@bgu.ac.il
> Phone: 972-8-647-2220  Skype: boaz.shaanan  
> Fax:   972-8-647-2992 or 972-8-646-1710
>  
>  
>  
> 
> ___
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[galaxy-dev] Local installation: Questions about using rsync to retrieve a genome

[Boaz Shaanan]

Hi,


1) I'd like to fetch the genome of H. salinarum NRC-1 on my local installation. Following your advice (http://wiki.galaxyproject.org/Admin/Data%20Integration

I wanted to use rsync. To begin with I tried the example in the above url, even though that's not the genome I'm interested in:
  

 rsync
 -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
 
I didn't get any response. My questions are:
1) Is it because the ftp site was not on ? Or could it be a firewall problem? Can the site be accessed in a different way that I can try?
2)Where can I find the file name where the H. salinarum NRC-1 genome resides on the server?


 Thanks for your help.


                                  Boaz


Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 










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Re: [galaxy-dev] Invalid Galaxy URL: None - Installing Tools Shed

[Greg Von Kuster]

You just need something like the following in your universe_wsgi.ini.

# Tool config files, defines what tools are available in Galaxy.
# Tools can be locally developed or installed from Galaxy tool sheds.
tool_config_file = tool_conf.xml,shed_tool_conf.xml



On Aug 6, 2013, at 1:27 PM, Peter Cock  wrote:

> On Tue, Aug 6, 2013 at 6:22 PM, Greg Von Kuster  wrote:
>> 
>> On Aug 6, 2013, at 1:14 PM, Peter Cock  wrote:
>> 
>>> My Firefox is setup to accept cookies until the expire, but not
>>> to accept third-party cookies.
>>> 
>>> Do I need to worry about cross-site cookies for my Galaxy server
>>> talking to the Main (or Test) Tool Shed?
>>> 
>> 
>> Yes, this must be the problem - third-party cookies are used to store
>> information between the Galaxy and Tool Shed applications.
>> 
> 
> Confirmed, I relaxed the 3rd party cookie setting to "from visited",
> now I get a new error message which is much easier to understand
> (and which I will look at tomorrow):
> 
> 
> The tool_config_file setting in universe_wsgi.ini must include at
> least one shed tool configuration file name with a  tag that
> includes a tool_path attribute value which is a directory relative to
> the Galaxy installation directory in order to automatically install
> tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml
> whose  tag is ).
> 
> See the Installation of Galaxy tool shed repository tools into a local
> Galaxy instance section of the Galaxy tool shed wiki for all of the
> details.
> 
> 
> Getting back to the cookie problem, perhaps the error message
> could use the phrase "third-party cookies" rather than just
> plain "cookies"?
> 
> Thanks,
> 
> Peter

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Re: [galaxy-dev] Invalid Galaxy URL: None - Installing Tools Shed

[Peter Cock]

On Tue, Aug 6, 2013 at 6:22 PM, Greg Von Kuster  wrote:
>
> On Aug 6, 2013, at 1:14 PM, Peter Cock  wrote:
>
>> My Firefox is setup to accept cookies until the expire, but not
>> to accept third-party cookies.
>>
>> Do I need to worry about cross-site cookies for my Galaxy server
>> talking to the Main (or Test) Tool Shed?
>>
>
> Yes, this must be the problem - third-party cookies are used to store
> information between the Galaxy and Tool Shed applications.
>

Confirmed, I relaxed the 3rd party cookie setting to "from visited",
now I get a new error message which is much easier to understand
(and which I will look at tomorrow):


The tool_config_file setting in universe_wsgi.ini must include at
least one shed tool configuration file name with a  tag that
includes a tool_path attribute value which is a directory relative to
the Galaxy installation directory in order to automatically install
tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml
whose  tag is ).

See the Installation of Galaxy tool shed repository tools into a local
Galaxy instance section of the Galaxy tool shed wiki for all of the
details.


Getting back to the cookie problem, perhaps the error message
could use the phrase "third-party cookies" rather than just
plain "cookies"?

Thanks,

Peter
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Re: [galaxy-dev] Invalid Galaxy URL: None - Installing Tools Shed

[Greg Von Kuster]

On Aug 6, 2013, at 1:14 PM, Peter Cock  wrote:

> My Firefox is setup to accept cookies until the expire, but not
> to accept third-party cookies.
> 
> Do I need to worry about cross-site cookies for my Galaxy server
> talking to the Main (or Test) Tool Shed?
> 

Yes, this must be the problem - third-party cookies are used to store 
information between the Galaxy and Tool Shed applications.


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Re: [galaxy-dev] Invalid Galaxy URL: None - Installing Tools Shed

[Peter Cock]

On Tue, Aug 6, 2013 at 6:11 PM, Greg Von Kuster  wrote:
> Hi peter,
>
> Do you have cookies blocked in your Firefox browser?  Does your
> cookie_path setting work for what you've configured in your apache
> prefix?

Yes, logging into my Galaxy and using it works fine - I can close
tabs and go back and still be logged in.

> It's impossible to tell what specifically could be causing this
> in your environment, but it's definitely related to cookies.
>
> Greg Von Kuster

My Firefox is setup to accept cookies until the expire, but not
to accept third-party cookies.

Do I need to worry about cross-site cookies for my Galaxy server
talking to the Main (or Test) Tool Shed?

Peter
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Re: [galaxy-dev] Invalid Galaxy URL: None - Installing Tools Shed

[Greg Von Kuster]

Hi peter,

Do you have cookies blocked in your Firefox browser?  Does your cookie_path 
setting work for what you've configured in your apache prefix?  It's impossible 
to tell what specifically could be causing this in your environment, but it's 
definitely related to cookies.

Greg Von Kuster


On Aug 6, 2013, at 12:57 PM, Peter Cock  wrote:

> Hi all,
> 
> I'm (finally) attempting to install a tool from the main Tool Shed into
> a local Galaxy instance, using Firefox, and got the same red error
> that Adam reported (below):
> 
> "Repository installation is not possible due to an invalid Galaxy URL:
> None. You may need to enable cookies in your browser."
> 
> Might my apache rewrite be causing this? My galaxy server is
> available on the normal http port 80 as servername/galaxy and
> in universe_wsgi.ini I have set:
> 
> cookie_path = /galaxy
> 
> Is there another setting which I need to fill in (perhaps something
> missing in older copies of universe_wsgi.ini.sample)?
> 
> Thanks,
> 
> Peter
> 
> On Wed, May 8, 2013 at 2:45 PM, Dave Bouvier  wrote:
>> Adam,
>> 
>> Normally, the Galaxy URL should be automatically determined and set in a
>> cookie during the repository installation process.
>> 
>> To help track down this issue, could you provide the revision of Galaxy
>> you're running, and the end of the paster.log file when this error occurs?
>> 
>> 
>>   --Dave B.
>> 
>> 
>> On 5/7/13 20:13:38.000, Adam Brenner wrote:
>>> 
>>> Howdy,
>>> 
>>> I am trying to install a tools shed item, Emboss, but when I do this
>>> via the admin interface, I get the following text:
>>> 
>>> Repository installation is not possible due to an invalid Galaxy URL:
>>> None. You may need to enable cookies in your browser.
>>> 
>>> I have searched the universe_wsgi.ini file and could not find anything
>>> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
>>> 
>>> Thanks,
>>> -Adam
>>> 
>>> --
>>> Adam Brenner
>>> Computer Science, Undergraduate Student
>>> Donald Bren School of Information and Computer Sciences
>>> 
>>> Research Computing Support
>>> Office of Information Technology
>>> http://www.oit.uci.edu/rcs/
>>> 
>>> University of California, Irvine
>>> www.ics.uci.edu/~aebrenne/
>>> aebre...@uci.edu
>>> ___
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>>> 
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Re: [galaxy-dev] Invalid Galaxy URL: None - Installing Tools Shed

[Peter Cock]

Hi all,

I'm (finally) attempting to install a tool from the main Tool Shed into
a local Galaxy instance, using Firefox, and got the same red error
that Adam reported (below):

"Repository installation is not possible due to an invalid Galaxy URL:
None. You may need to enable cookies in your browser."

Might my apache rewrite be causing this? My galaxy server is
available on the normal http port 80 as servername/galaxy and
in universe_wsgi.ini I have set:

cookie_path = /galaxy

Is there another setting which I need to fill in (perhaps something
missing in older copies of universe_wsgi.ini.sample)?

Thanks,

Peter

On Wed, May 8, 2013 at 2:45 PM, Dave Bouvier  wrote:
> Adam,
>
> Normally, the Galaxy URL should be automatically determined and set in a
> cookie during the repository installation process.
>
> To help track down this issue, could you provide the revision of Galaxy
> you're running, and the end of the paster.log file when this error occurs?
>
>
>--Dave B.
>
>
> On 5/7/13 20:13:38.000, Adam Brenner wrote:
>>
>> Howdy,
>>
>> I am trying to install a tools shed item, Emboss, but when I do this
>> via the admin interface, I get the following text:
>>
>> Repository installation is not possible due to an invalid Galaxy URL:
>> None. You may need to enable cookies in your browser.
>>
>> I have searched the universe_wsgi.ini file and could not find anything
>> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
>>
>> Thanks,
>> -Adam
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> Research Computing Support
>> Office of Information Technology
>> http://www.oit.uci.edu/rcs/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> aebre...@uci.edu
>> ___
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Peter Cock]

On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo  wrote:
> Dave,
>
> It did contain errors as reported by tailing the last part of the
> INSTALLATION.log
>
> Thanks
>
> --Rodolfo

Looks like your BOOST is too new for BLAST 2.2.26+ (which
just recently became a problem on the Galaxy Tool Shed testing
system as well).

In the short term I'm hoping to update the Tool Shed repository
to use the NCBI provided pre-compiled binaries. I'm in discussion
with Galaxy's Dave Bouvier about how best to do that, perhaps
with some relatively new functionality added to Galaxy. Next,
updating the BLAST+ version (and the unit tests to match).

I would suggest right now you manually install BLAST+ using
the NCBI provided binaries.

Peter
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Greg Von Kuster]

Hi Rodolfo,

There was a bug with regard to displaying the Installation status of a tool 
dcependency installed into Galaxy along with a repository from the Tool Shed.  
I have corrected this bug in the mentioned change set, so if you upgrade your 
Galaxy code to the mentioned revision, the installation status will now be 
displayed.

Greg Von Kuster

On Aug 6, 2013, at 10:29 AM, Rodolfo Aramayo  wrote:

> You are very welcome
> So...what happened??
> Thanks
> 
> --R
> 
> On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster  wrote:
>> Hello Rodolfo,
>> 
>> The following issue is resolved in 10319:61de03c05cf6 - thank for reporting 
>> this.
>> 
>> Greg Von Kuster
>> 
>> On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo  wrote:
>> 
>>> 
>>> I did and it worked well it installed Blast 2.2.26+
>>> 
>>> However there are two problems:
>>> 
>>> 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'"
>>> The name, Version and Type display correct values. However the
>>> 'Installation status' shows no text
>> 
>> 
>> 
>> 
>> 
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Re: [galaxy-dev] datatype logic

[Jeremy Goecks]

> If I share a history, it produces a url with the datasets. This is good. But 
> if you click on the eyeball in this view, it shows the dataset in its raw 
> form. Its as if the code path does not go through the sophisticated datatype 
> logic. Is this deliberate or an oversight?

Incomplete integration of the new display code. We would welcome a Trello card 
or pull request to resolve this issue.

Best,
J.
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Rodolfo Aramayo]

You are very welcome
So...what happened??
Thanks

--R

On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster  wrote:
> Hello Rodolfo,
>
> The following issue is resolved in 10319:61de03c05cf6 - thank for reporting 
> this.
>
> Greg Von Kuster
>
> On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo  wrote:
>
>>
>> I did and it worked well it installed Blast 2.2.26+
>>
>> However there are two problems:
>>
>> 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'"
>> The name, Version and Type display correct values. However the
>> 'Installation status' shows no text
>
>
>
>
>
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Greg Von Kuster]

Hello Rodolfo,

The following issue is resolved in 10319:61de03c05cf6 - thank for reporting 
this.

Greg Von Kuster

On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo  wrote:

> 
> I did and it worked well it installed Blast 2.2.26+
> 
> However there are two problems:
> 
> 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'"
> The name, Version and Type display correct values. However the
> 'Installation status' shows no text






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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Dave Bouvier]

Rodolfo,

   --Dave B.

On 8/5/13 15:50:46.000, Rodolfo Aramayo wrote:

Dave,

See below

On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier  wrote:

Rodolfo,

Please keep the thread on the mailing list by using the "Reply all" option.


Apologies



You should now be able to go to the manage repository page, select the tool
dependency, then select 'Manage tool dependencies' from the repository
actions dropdown and reinstall the blast+ tool dependency.

--Dave B.



I did and it worked well it installed Blast 2.2.26+

However there are two problems:

1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'"
The name, Version and Type display correct values. However the
'Installation status' shows no text

2. When I run the same blast job I was able to run before (using
Blast+ 2.2.28+...that I installed) I get the following:

error
An error occurred with this dataset: blastn: 2.2.26+ Package: blast
2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error:
NCBI C++ Exception:
"/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
line 689: Critical:


Obviously it is the installed Blast that is at fault in here



Did the blast+ tool dependency compile without errors? You should be 
able to see any errors by clicking on the installed tool dependency, 
then expanding the blast+ folder and clicking on INSTALLATION.log



Thanks

--R



On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:


Dear Dave,

Answers below...

On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier  wrote:


Rodolfo,

In order to simplify tracking down this issue, could you provide the
changeset revision of Galaxy that is running on tamu.edu? To retrieve the
revision, execute the following command in your galaxy root directory:

hg id



fd4113962c32+ (stable)



To clarify, our understanding is that you installed the ncbi_blast_plus
repository from the main tool shed, and it installed correctly. You then
uninstalled the repository, and it also uninstalled properly. You then
attempted to reinstall the repository, and encountered the error message
cited in your email.

Can you confirm the above?



This is correct



We further understand that the repository is stuck in the 'installing'
state.



YES and in the "Manage installed tool shed repositories" says now
(after having to restart Galaxy for another reason):

"Installed, Missing tool dependencies"


What options are available from the popup menu next to the


ncbi_blast_plus repository on the manage installed repositories page?



   If I click on the little arrow, it says:

Get updates
Deactivate or uninstall


'Deactivate or uninstall' is available, can you try uninstalling again,
and
see if that functions correctly?



It worked!

Before I was not able to do it as I was getting an ugly galaxy error page
But now it did uninstall and removed and was able to clone correctly.
However, the directory:


./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/

is empty!


Should I repopulate it with the one I have in my backup??

Thanks

--Rodolfo




 --Dave B.


On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:



People,

I successfully installed NCBI_Blast_Plus from the toolshed
The tool, however, failed to work giving the following error:

Fatal error: Exit code 255 ()
Error: NCBI C++ Exception:


"/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
Attempt to access NULL pointer.

I then tried uninstalling/reinstalling the tool

However I now get an eternal 'installing' grey message and when I
click 'manage the repo' I get:

#

URL:

http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
File

'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
 app_iter = self.application(environ, sr_checker)
File

'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
 return self.application(environ, start_response)
File

'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
 return self.application(environ, start_response)
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
 return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
 body = method( trans, **kwargs )
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 221 in decorator
 return func( self, trans, *args, **kwargs )
File

'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 561 in manage_repository
 repository = suc.get_installed_tool_shed_repository( trans,
repository_id )
File
'/usr/

Re: [galaxy-dev] getting large files into a local instance of Galaxy

[Hans-Rudolf Hotz]

Hi Gerald

Have you looked into 'Data Libraries'?

http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

This will allow you to access the files without data duplication.

Regards, Hans-Rudolf


On 08/05/2013 08:48 PM, Gerald Bothe wrote:

Trying out a local instance of Galaxy. Small files can be uploaded with
"browse.." but this works only for files under 2Gb. Is there a folder in
a local copy of galaxy-dist where I can copy a large file and have it
show up in the Get Data/Upload File/Files uploaded via FTP window so
that I can properly get it into the local history? Copying it directly
into the database seemed not to work, it didn't show up anywhere.
Gerald

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Re: [galaxy-dev] Mail is not configured for this Galaxy instance.

[Hans-Rudolf Hotz]

On 08/06/2013 08:17 AM, shenwiyn wrote:

Hi Hans-Rudolf,
Thank you very much for you help.Actually I want some more information
about how to configure 'smtp_server' in "universe_wsgi.ini".Could you
show me some samples to have a look please?



you need the address of your smtp server, eg:

smtp_server = abcd.fmi.ch





Regards, shenwiyn
*From:* Hans-Rudolf Hotz 
*Date:* 2013-07-31 23:40
*To:* shenwiyn 
*CC:* galaxy-dev@lists.bx.psu.edu 
*Subject:* Re: [galaxy-dev] Mail is not configured for this Galaxy instance.
Hi Shenwiyn
You need to specify a SMTP server. Have a look at the 'smtp_server'
settings in your "universe_wsgi.ini" file.
Regards, Hans-Rudolf
On 07/31/2013 04:19 PM, shenwiyn wrote:
 > Hi everyone,
 > In my local Galaxy,when I want to reset my Login password,some error
 > occurre
 > :"Mail is not configured for this Galaxy instance. Please contact an 
administrator.
 > "Could anyone tell me some imformation about how to configure the mail
 > for my Galaxy instance?
 > Thank you very much.
 > 
 > shenwiyn
 >
 >
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