You can propose some updates (ie: URL) in this GitHub repo : https://github.com/galaxyproject/cargo-port <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 <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 <peter.briggs@manchester.ac.uk> 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_s...

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-lin...

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

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/

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-- Peter Briggs peter.briggs@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/

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.briggs@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_sequenc e_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 <peter.briggs@manchester.ac.uk

...

<mailto:peter.briggs@manchester.ac.uk>> 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_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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

-- Peter Briggs peter.briggs@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.briggs@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/

Thanks for the update Nate, glad you were able to fix it! Best wishes Peter -- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ________________________________ From: Nate Coraor [nate@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.briggs@manchester.ac.uk<mailto:peter.briggs@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_s... ... <time passes> ... --2016-12-19 10:20:47-- (try:20) http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_s... 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.briggs@manchester.ac.uk<mailto:peter.briggs@manchester.ac.uk> <mailto:peter.briggs@manchester.ac.uk<mailto:peter.briggs@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_s... 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-lin... package_samtools_0_1_19 Exception: Error downloading from URL https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.ta... * 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.briggs@manchester.ac.uk<mailto:peter.briggs@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.briggs@manchester.ac.uk<mailto:peter.briggs@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/