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
I forgot to mention, both server and cluster are running under CentOS 7. The Galaxy version is release_18.09 ________________________________________ De : galaxy-dev <galaxy-dev-bounces@lists.galaxyproject.org> de la part de Estelle Ancelet <estelle.ancelet@inra.fr> Envoyé : mercredi 12 décembre 2018 10:17 À : galaxy-dev@lists.galaxyproject.org 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/
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 : galaxy-dev@lists.galaxyproject.org 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 <galaxy-dev-bounces@lists.galaxyproject.org> de la part de Estelle Ancelet <estelle.ancelet@inra.fr> Envoyé : mercredi 12 décembre 2018 10:17 À : galaxy-dev@lists.galaxyproject.org 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/
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Estelle Ancelet