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Installation of packages failing

jamesp
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.

Regards
​James

J P Mullan

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Re: Installation of packages failing

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
>
>
> ___________________________________________________________
> 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 [hidden email]
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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Re: Installation of packages failing

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 <[hidden email]> 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 [hidden email]
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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Installation of packages failing

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
...
<time passes>
...
--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 <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 <[hidden email]
>> <mailto:[hidden email]>> a écrit :
>>
>> Hello James
>>
>> I think this might be a general problem with 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
>>>
>>>
>>> ___________________________________________________________
>>> 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 [hidden email]
>> 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 [hidden email]
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: Installation of packages failing

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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
...
<time passes>
...
--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 <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: <a href="tel:%2B33%202%2098%2029%2023%2081" value="+33298292381" target="_blank">+33 2 98 29 23 81
------------------------------------------------------------------



Le 19 déc. 2016 à 10:42, Peter Briggs <[hidden email]
<mailto:[hidden email]>> a écrit :

Hello James

I think this might be a general problem with 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


___________________________________________________________
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 [hidden email]
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 [hidden email]
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/


___________________________________________________________
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: Installation of packages failing

jamesp
Many Thanks Nate,
                         my bowtie dependency is installed now.

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/
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Re: Installation of packages failing

Peter Briggs
In reply to this post by Nate Coraor (nate@bx.psu.edu)
Thanks for the update Nate, glad you were able to fix it!
Best wishes
Peter

-- 
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


From: Nate Coraor [[hidden email]]
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 <[hidden email]> 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
...
<time passes>
...
--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 <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: <a href="tel:%2B33%202%2098%2029%2023%2081" value="&#43;33298292381" target="_blank"> +33 2 98 29 23 81
------------------------------------------------------------------



Le 19 déc. 2016 à 10:42, Peter Briggs <[hidden email]
<mailto:[hidden email]>> a écrit :

Hello James

I think this might be a general problem with 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


___________________________________________________________
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 [hidden email]
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 [hidden email]
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/


___________________________________________________________
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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