cyverse-ansible.singularity

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cyverse-ansible.singularity

Luc Cornet
Hello all,

I have a problem with singularity while installing galaxy with ansible.

```
ASK [cyverse-ansible.singularity : Ubuntu package installation for v3.0 or newer] *************************************************************************
ok: [galaxy.inbios.uliege.be]

TASK [cyverse-ansible.singularity : CentOS package installation for v3.0 or newer] *************************************************************************
skipping: [galaxy.inbios.uliege.be]

TASK [cyverse-ansible.singularity : check if singularity binary exists] ************************************************************************************
ok: [galaxy.inbios.uliege.be]

TASK [cyverse-ansible.singularity : Obtain current binary version] *****************************************************************************************
skipping: [galaxy.inbios.uliege.be]

TASK [cyverse-ansible.singularity : download the singularity release] **************************************************************************************
fatal: [galaxy.inbios.uliege.be]: FAILED! => {"changed": false, "dest": "/tmp/singularity-3.7.0.tar.gz", "elapsed": 5, "msg": "Request failed", "response": "HTTP Error 404: Not Found", "status_code": 404, "url": "https://github.com/sylabs/singularity/releases/download/v3.7.0/singularity-3.7.0.tar.gz"}
```

The URL for singularity has changed, Do you know how can i fix that ?


Maybe a more recent version of :

```
- src: cyverse-ansible.singularity
version: 048c4f178077d05c1e67ae8d9893809aac9ab3b7
```

Thanks for the help,  
Luc

------------
Luc Cornet, PhD
Bio-informatician
Mycology and Aerobiology
Sciensano
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Re: cyverse-ansible.singularity

Keith Suderman-3
Hi Luc,

The version used in our playbook actually references one of our pull requests [1] and it looks like it references the most recent version.  However, even the most recent playbook on GitHub uses the incorrect URL.  Something must have changed since January.

In the interim you could try editing the role locally.  In the roles/cyverse-ansible.singularity/tasks/singularity-post-3.yml fie (or, or around line 47) change:

    url: "https://github.com/sylabs/singularity/releases/download/v{{singularity_version}}/singularity-{{singularity_version}}.tar.gz"

to:
    url: https://github.com/sylabs/singularity/archive/refs/tags/v{{ singularity_version }}.tar.gz


I haven't had a chance to actually test that, but it should pull the correct tarball.

Cheers,
Keith

1. https://github.com/galaxyproject/training-material/pull/2269


> On May 7, 2021, at 9:24 AM, Luc Cornet <[hidden email]> wrote:
>
>
>      External Email - Use Caution
>
>
>
> Hello all,
>
> I have a problem with singularity while installing galaxy with ansible.
>
> ```
> ASK [cyverse-ansible.singularity : Ubuntu package installation for v3.0 or newer] *************************************************************************
> ok: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : CentOS package installation for v3.0 or newer] *************************************************************************
> skipping: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : check if singularity binary exists] ************************************************************************************
> ok: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : Obtain current binary version] *****************************************************************************************
> skipping: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : download the singularity release] **************************************************************************************
> fatal: [galaxy.inbios.uliege.be]: FAILED! => {"changed": false, "dest": "/tmp/singularity-3.7.0.tar.gz", "elapsed": 5, "msg": "Request failed", "response": "HTTP Error 404: Not Found", "status_code": 404, "url": "https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsylabs%2Fsingularity%2Freleases%2Fdownload%2Fv3.7.0%2Fsingularity-3.7.0.tar.gz&amp;data=04%7C01%7Csuderman%40jhu.edu%7C43edc9785a1246f3b79a08d9116411fc%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637559943775184956%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=DZ5eYAoCSsZHRgHl7BnnGwyER%2Fcyv2RuNCn5KEZG8nw%3D&amp;reserved=0"}
> ```
>
> The URL for singularity has changed, Do you know how can i fix that ?
>
>
> Maybe a more recent version of :
>
> ```
> - src: cyverse-ansible.singularity
> version: 048c4f178077d05c1e67ae8d9893809aac9ab3b7
> ```
>
> Thanks for the help,
> Luc
>
> ------------
> Luc Cornet, PhD
> Bio-informatician
> Mycology and Aerobiology
> Sciensano
> ___________________________________________________________
> 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:
>  %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>  https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgalaxyproject.org%2Fsearch%2F&amp;data=04%7C01%7Csuderman%40jhu.edu%7C43edc9785a1246f3b79a08d9116411fc%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637559943775184956%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=6%2BNoAtq58508X9vNI4ijTiTsr%2BCCPEPk8vyVAL7K82Q%3D&amp;reserved=0
___________________________________________________________
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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Re: cyverse-ansible.singularity

Luc Cornet
Re,

I found an explanation but not a solution :

https://groups.google.com/a/lbl.gov/g/singularity/c/VN3WL5dBrUs


This is most commonly due to downloading GitHub's auto generated 'source code' tarball, which contains all the files in the Git repository, but is not a git repo, nor contains the extra things added when we create a release.

Check that you are using the tarball from: https://github.com/hpcng/singularity/releases/tag/v3.6.4 that is called `singularity-3.6.4.tar.gz` and not the `Source code (tar.gz) link`. There's also a sha256sums file there so you can check the hash of the tarball you have to make sure it is correct.

The correct one does have the VERSION file referred to, and the vendored libraries etc. that are needed to build outside of a git clone.


Best,
Luc

------------
Luc Cornet, PhD
Bio-informatician
Mycology and Aerobiology
Sciensano

----- Mail original -----
De: "Keith Suderman" <[hidden email]>
À: "Luc Cornet" <[hidden email]>
Cc: "HelpGalaxy" <[hidden email]>
Envoyé: Dimanche 9 Mai 2021 20:38:49
Objet: Re: [galaxy-dev] cyverse-ansible.singularity

Hi Luc,

The version used in our playbook actually references one of our pull requests [1] and it looks like it references the most recent version.  However, even the most recent playbook on GitHub uses the incorrect URL.  Something must have changed since January.

In the interim you could try editing the role locally.  In the roles/cyverse-ansible.singularity/tasks/singularity-post-3.yml fie (or, or around line 47) change:

    url: "https://github.com/sylabs/singularity/releases/download/v{{singularity_version}}/singularity-{{singularity_version}}.tar.gz"

to:
    url: https://github.com/sylabs/singularity/archive/refs/tags/v{{ singularity_version }}.tar.gz


I haven't had a chance to actually test that, but it should pull the correct tarball.

Cheers,
Keith

1. https://github.com/galaxyproject/training-material/pull/2269


> On May 7, 2021, at 9:24 AM, Luc Cornet <[hidden email]> wrote:
>
>
>      External Email - Use Caution
>
>
>
> Hello all,
>
> I have a problem with singularity while installing galaxy with ansible.
>
> ```
> ASK [cyverse-ansible.singularity : Ubuntu package installation for v3.0 or newer] *************************************************************************
> ok: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : CentOS package installation for v3.0 or newer] *************************************************************************
> skipping: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : check if singularity binary exists] ************************************************************************************
> ok: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : Obtain current binary version] *****************************************************************************************
> skipping: [galaxy.inbios.uliege.be]
>
> TASK [cyverse-ansible.singularity : download the singularity release] **************************************************************************************
> fatal: [galaxy.inbios.uliege.be]: FAILED! => {"changed": false, "dest": "/tmp/singularity-3.7.0.tar.gz", "elapsed": 5, "msg": "Request failed", "response": "HTTP Error 404: Not Found", "status_code": 404, "url": "https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsylabs%2Fsingularity%2Freleases%2Fdownload%2Fv3.7.0%2Fsingularity-3.7.0.tar.gz&amp;data=04%7C01%7Csuderman%40jhu.edu%7C43edc9785a1246f3b79a08d9116411fc%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637559943775184956%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=DZ5eYAoCSsZHRgHl7BnnGwyER%2Fcyv2RuNCn5KEZG8nw%3D&amp;reserved=0"}
> ```
>
> The URL for singularity has changed, Do you know how can i fix that ?
>
>
> Maybe a more recent version of :
>
> ```
> - src: cyverse-ansible.singularity
> version: 048c4f178077d05c1e67ae8d9893809aac9ab3b7
> ```
>
> Thanks for the help,
> Luc
>
> ------------
> Luc Cornet, PhD
> Bio-informatician
> Mycology and Aerobiology
> Sciensano
> ___________________________________________________________
> 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:
>  %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>  https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgalaxyproject.org%2Fsearch%2F&amp;data=04%7C01%7Csuderman%40jhu.edu%7C43edc9785a1246f3b79a08d9116411fc%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637559943775184956%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=6%2BNoAtq58508X9vNI4ijTiTsr%2BCCPEPk8vyVAL7K82Q%3D&amp;reserved=0
___________________________________________________________
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:
  %(web_page_url)s

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