Re: [galaxy-dev] Installation of packages failing

2016-12-19 Thread Peter Briggs 
Thanks for the update Nate, glad you were able to fix it!
Best wishes
Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


From: Nate Coraor [n...@bx.psu.edu]
Sent: Monday, December 19, 2016 5:08 PM
To: Peter Briggs
Cc: Gildas Le Corguillé; James Mullan; Galaxy Dev List
Subject: Re: [galaxy-dev] Installation of packages failing

Hi Peter, Gildas,

This was due to a power supply failure which we've fixed this morning, so this 
should all be working now.

Thanks,
--nate

On Mon, Dec 19, 2016 at 5:46 AM, Peter Briggs 
<peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>> wrote:
Hello Gildas

I think the problem is more that the actual server isn't serving the packages 
that are already hosted there.

For example:

$ wget 
http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz
...

...
--2016-12-19 10:20:47--  (try:20) 
http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz
Connecting to depot.galaxyproject.org<http://depot.galaxyproject.org> 
(depot.galaxyproject.org<http://depot.galaxyproject.org>)|128.118.250.14|:80... 
failed: Connection timed out.
Giving up.

I tried this from a few different locations last week with the same result.

Best wishes

Peter

On 19/12/16 10:08, Gildas Le Corguillé wrote:
You can propose some updates (ie: URL) in this GitHub repo
: https://github.com/galaxyproject/cargo-port

Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81<tel:%2B33%202%2098%2029%2023%2081>
--



Le 19 déc. 2016 à 10:42, Peter Briggs 
<peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>
<mailto:peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>>> a 
écrit :

Hello James

I think this might be a general problem with 
depot.galaxyproject.org<http://depot.galaxyproject.org>
<http://depot.galaxyproject.org> serving packages, as I've been

experiencing similar problems since Friday - attempts to fetch e.g.

http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz

also fail with timeouts.

I guess it needs someone from the the Galaxy project to take a look,

Best wishes

Peter

On 18/12/16 20:25, James Mullan wrote:
Hello,*
*
* *  I am trying to install packages with dependencies from
Galaxy Main tool shed.
This worked Thursday and since Friday it no longer works for me.
It seems this url is no longer reachable. Examples of what I see in the
log during download are shown below.

Any help would be much appreciated.

package_bowtie_0_12_7
Error downloading from URL
http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz

package_samtools_0_1_19
Exception: Error downloading from URL
https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2*
*

Regards
​James

J P Mullan


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--
Peter Briggs peter.bri...@manchester.ac.uk<mailto: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<mailto: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] Installation of packages failing

2016-12-19 Thread James Mullan 
Many Thanks Nate,
 my bowtie dependency is installed now.

Regards

​James​

J P Mullan
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Re: [galaxy-dev] Installation of packages failing

2016-12-19 Thread Nate Coraor 
Hi Peter, Gildas,

This was due to a power supply failure which we've fixed this morning, so
this should all be working now.

Thanks,
--nate

On Mon, Dec 19, 2016 at 5:46 AM, Peter Briggs  wrote:

> Hello Gildas
>
> I think the problem is more that the actual server isn't serving the
> packages that are already hosted there.
>
> For example:
>
> $ wget http://depot.galaxyproject.org/package/source/galaxy_sequenc
> e_utils/galaxy_sequence_utils-1.0.1-st.tgz
> ...
> 
> ...
> --2016-12-19 10:20:47--  (try:20) http://depot.galaxyproject.org
> /package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz
> Connecting to depot.galaxyproject.org 
> (depot.galaxyproject.org)|128.118.250.14|:80...
> failed: Connection timed out.
> Giving up.
>
> I tried this from a few different locations last week with the same result.
>
> Best wishes
>
> Peter
>
> On 19/12/16 10:08, Gildas Le Corguillé wrote:
>
>> You can propose some updates (ie: URL) in this GitHub repo
>> : https://github.com/galaxyproject/cargo-port
>>
>> Cheers
>>
>> Gildas
>>
>> -
>> Gildas Le Corguillé - Bioinformatician/Bioanalyste
>>
>> Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
>> http://abims.sb-roscoff.fr
>>
>> Member of the Workflow4Metabolomics project
>> http://workflow4metabolomics.org 
>>
>> Station Biologique de Roscoff - UPMC/CNRS - FR2424
>> Place Georges Teissier 29680 Roscoff FRANCE
>> tel: +33 2 98 29 23 81
>> --
>>
>>
>>
>> Le 19 déc. 2016 à 10:42, Peter Briggs >> > a écrit :
>>>
>>> Hello James
>>>
>>> I think this might be a general problem with depot.galaxyproject.org
>>>  serving packages, as I've been
>>>
>>> experiencing similar problems since Friday - attempts to fetch e.g.
>>>
>>> http://depot.galaxyproject.org/package/source/galaxy_sequenc
>>> e_utils/galaxy_sequence_utils-1.0.1-st.tgz
>>>
>>> also fail with timeouts.
>>>
>>> I guess it needs someone from the the Galaxy project to take a look,
>>>
>>> Best wishes
>>>
>>> Peter
>>>
>>> On 18/12/16 20:25, James Mullan wrote:
>>>
 Hello,*
 *
 * *  I am trying to install packages with dependencies from
 Galaxy Main tool shed.
 This worked Thursday and since Friday it no longer works for me.
 It seems this url is no longer reachable. Examples of what I see in the
 log during download are shown below.

 Any help would be much appreciated.

 package_bowtie_0_12_7
 Error downloading from URL
 http://depot.galaxyproject.org/package/linux/x86_64/bowtie/
 bowtie-0.12.7-linux-x86_64.tgz

 package_samtools_0_1_19
 Exception: Error downloading from URL
 https://depot.galaxyproject.org/software/samtools/samtools_
 0.1.19_src_all.tar.bz2*
 *

 Regards
 ​James

 J P Mullan


 ___
 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:
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 To search Galaxy mailing lists use the unified search at:
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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
>>> ___
>>> 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:
>>> https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> ___
> 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:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] Installation of packages failing

2016-12-19 Thread Peter Briggs 

Hello Gildas

I think the problem is more that the actual server isn't serving the 
packages that are already hosted there.


For example:

$ wget 
http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz

...

...
--2016-12-19 10:20:47--  (try:20) 
http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz
Connecting to depot.galaxyproject.org 
(depot.galaxyproject.org)|128.118.250.14|:80... failed: Connection timed 
out.

Giving up.

I tried this from a few different locations last week with the same result.

Best wishes

Peter

On 19/12/16 10:08, Gildas Le Corguillé wrote:

You can propose some updates (ie: URL) in this GitHub repo
: https://github.com/galaxyproject/cargo-port

Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org 

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--




Le 19 déc. 2016 à 10:42, Peter Briggs > a écrit :

Hello James

I think this might be a general problem with depot.galaxyproject.org
 serving packages, as I've been
experiencing similar problems since Friday - attempts to fetch e.g.

http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz

also fail with timeouts.

I guess it needs someone from the the Galaxy project to take a look,

Best wishes

Peter

On 18/12/16 20:25, James Mullan wrote:

Hello,*
*
* *  I am trying to install packages with dependencies from
Galaxy Main tool shed.
This worked Thursday and since Friday it no longer works for me.
It seems this url is no longer reachable. Examples of what I see in the
log during download are shown below.

Any help would be much appreciated.

package_bowtie_0_12_7
Error downloading from URL
http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz

package_samtools_0_1_19
Exception: Error downloading from URL
https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2*
*

Regards
​James

J P Mullan


___
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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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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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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in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Installation of packages failing

2016-12-19 Thread Gildas Le Corguillé 
You can propose some updates (ie: URL) in this GitHub repo : 
https://github.com/galaxyproject/cargo-port 


Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr 

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org 

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 19 déc. 2016 à 10:42, Peter Briggs  a écrit 
> :
> 
> Hello James
> 
> I think this might be a general problem with depot.galaxyproject.org serving 
> packages, as I've been experiencing similar problems since Friday - attempts 
> to fetch e.g.
> 
> http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz
> 
> also fail with timeouts.
> 
> I guess it needs someone from the the Galaxy project to take a look,
> 
> Best wishes
> 
> Peter
> 
> On 18/12/16 20:25, James Mullan wrote:
>> Hello,*
>> *
>> * *  I am trying to install packages with dependencies from
>> Galaxy Main tool shed.
>> This worked Thursday and since Friday it no longer works for me.
>> It seems this url is no longer reachable. Examples of what I see in the
>> log during download are shown below.
>> 
>> Any help would be much appreciated.
>> 
>> package_bowtie_0_12_7
>> Error downloading from URL
>> http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz
>> 
>> package_samtools_0_1_19
>> Exception: Error downloading from URL
>> https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2*
>> *
>> 
>> Regards
>> ​James
>> 
>> J P Mullan
>> 
>> 
>> ___
>> 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:
>>  https://lists.galaxyproject.org/
>> 
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/
>> 
> 
> -- 
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> ___
> 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:
> https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/

___
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Re: [galaxy-dev] Installation of packages failing

2016-12-19 Thread Peter Briggs 

Hello James

I think this might be a general problem with depot.galaxyproject.org 
serving packages, as I've been experiencing similar problems since 
Friday - attempts to fetch e.g.


http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz

also fail with timeouts.

I guess it needs someone from the the Galaxy project to take a look,

Best wishes

Peter

On 18/12/16 20:25, James Mullan wrote:

Hello,*
*
* *  I am trying to install packages with dependencies from
Galaxy Main tool shed.
This worked Thursday and since Friday it no longer works for me.
 It seems this url is no longer reachable. Examples of what I see in the
log during download are shown below.

Any help would be much appreciated.

package_bowtie_0_12_7
Error downloading from URL
http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz

package_samtools_0_1_19
Exception: Error downloading from URL
https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2*
*

Regards
​James

J P Mullan


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