Conda issue on a server using a sshfs mounting point

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Conda issue on a server using a sshfs mounting point

Estelle Ancelet
Hi Galaxy team,

I have a Galaxy server sharing a folder with a cluster through sshfs.
The Galaxy folder is cloned on the cluster : /home/galaxy-user/galaxy. On the server, I have the same directory but empty : /home/galaxy-user/galaxy.

On the server side, I use the following mounting command:
sshfs -o cache=no galaxy-user@clusterfr:galaxy galaxy

When I run galaxy (sh ./run.sh from galaxy-user in the VM), everything seems to go well but in fact, the _conda directory doesn’t contain any binary. It only contains the pkg folder.
The log message I get is “cannot install conda because conda_prefix /home/galaxy-user/galaxy/database/dependencies/_conda exists and is not empty”.

In the UI, if I try to install a tool with dependencies from the toolshed, I get the same log message.

I’ve also tried sshfs -o cache=no,idmap=user,allow_other.
But then, I cannot launch Galaxy. I have an arror (add error message).

Any clue on how to make conda work with this infrastructure?

Thanks in advance
Estelle
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Re: Conda issue on a server using a sshfs mounting point

Estelle Ancelet
I forgot to mention, both server and cluster are running under CentOS 7.
The Galaxy version is release_18.09

________________________________________
De : galaxy-dev <[hidden email]> de la part de Estelle Ancelet <[hidden email]>
Envoyé : mercredi 12 décembre 2018 10:17
À : [hidden email]
Objet : [galaxy-dev] Conda issue on a server using a sshfs mounting point

Hi Galaxy team,

I have a Galaxy server sharing a folder with a cluster through sshfs.
The Galaxy folder is cloned on the cluster : /home/galaxy-user/galaxy. On the server, I have the same directory but empty : /home/galaxy-user/galaxy.

On the server side, I use the following mounting command:
sshfs -o cache=no galaxy-user@clusterfr:galaxy galaxy

When I run galaxy (sh ./run.sh from galaxy-user in the VM), everything seems to go well but in fact, the _conda directory doesn’t contain any binary. It only contains the pkg folder.
The log message I get is “cannot install conda because conda_prefix /home/galaxy-user/galaxy/database/dependencies/_conda exists and is not empty”.

In the UI, if I try to install a tool with dependencies from the toolshed, I get the same log message.

I’ve also tried sshfs -o cache=no,idmap=user,allow_other.
But then, I cannot launch Galaxy. I have an arror (add error message).

Any clue on how to make conda work with this infrastructure?

Thanks in advance
Estelle
___________________________________________________________
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/
___________________________________________________________
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/
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Re: Conda issue on a server using a sshfs mounting point

Estelle Ancelet
Sorry, here is the error message I get with "sshfs -o cache=no,idmap=user,allow_other".

>>  Error: EACCES: permission denied, chown '/home/galaxy-user/galaxy/.venv/lib/node_modules/yarn/package.json.1508391558'

This message appears when I execute run.sh for the first time. Then the launching process is aborted.
________________________________________
De : Estelle Ancelet
Envoyé : mercredi 12 décembre 2018 10:20
À : [hidden email]
Objet : RE: Conda issue on a server using a sshfs mounting point

I forgot to mention, both server and cluster are running under CentOS 7.
The Galaxy version is release_18.09

________________________________________
De : galaxy-dev <[hidden email]> de la part de Estelle Ancelet <[hidden email]>
Envoyé : mercredi 12 décembre 2018 10:17
À : [hidden email]
Objet : [galaxy-dev] Conda issue on a server using a sshfs mounting point

Hi Galaxy team,

I have a Galaxy server sharing a folder with a cluster through sshfs.
The Galaxy folder is cloned on the cluster : /home/galaxy-user/galaxy. On the server, I have the same directory but empty : /home/galaxy-user/galaxy.

On the server side, I use the following mounting command:
sshfs -o cache=no galaxy-user@clusterfr:galaxy galaxy

When I run galaxy (sh ./run.sh from galaxy-user in the VM), everything seems to go well but in fact, the _conda directory doesn’t contain any binary. It only contains the pkg folder.
The log message I get is “cannot install conda because conda_prefix /home/galaxy-user/galaxy/database/dependencies/_conda exists and is not empty”.

In the UI, if I try to install a tool with dependencies from the toolshed, I get the same log message.

I’ve also tried sshfs -o cache=no,idmap=user,allow_other.
But then, I cannot launch Galaxy. I have an arror (add error message).

Any clue on how to make conda work with this infrastructure?

Thanks in advance
Estelle
___________________________________________________________
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/
___________________________________________________________
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/