Unable to fetch .......[Errno 28] No space left on device about docker-galaxy-stable HOT 21 CLOSED

Upload - How? Via FTP? Normal Galaxy web browser upload?

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Normal Galaxy via the button at the top of the main page with the arrow, pasting an http:// to the file via link to another machine in the network.

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I'm not aware of any limit with this. What you can do, you can log into the container and look what file system is full and adjust this.

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Do you know how to do that? I'm not familiar with this :)

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docker exec -i -t <container name> /bin/bash :)

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I got this:
Size Used Avail Use% Mounted on
/dev/mapper/docker-8:2-2148666710-4a4a5fff9c 9.8G 9.3G 20K 100% /
tmpfs 63G 0 63G 0% /dev
shm 64M 0 64M 0% /dev/shm
/dev/sdb1 21T 620G 20T 4% /export
/dev/sda2 542G 13G 530G 3% /data
tmpfs 63G 0 63G 0% /proc/kcore
tmpfs 63G 0 63G 0% /proc/timer_stats

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It looks like that tool stores things in /tmp, which doesn't have enough room.

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I see, so is there a way overpassing this, for example running the container with option for increased volume? I hope I'm not the only one with such issue. As my files usually are quite big (5-15GB), my preferred way of uploading will be as in this case.

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@ve379 your Docker container is using the filesystem from your host OS. So increasing the volume of you host OS will work. Otherwise you can try to mount in a new /tmp dir or try to set the $TMPDIR/$TMP/$TEMP environment variable to a bigger filesystem.

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But my host OS have more then 20TB free currently?!

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From what I see isn't the docker using by default 10GB? or I'm wrong (/dev/mapper/docker-8:2-2148666710-4a4a5fff9c 9.8G 9.3G(USED) 20K(FREE) 100% /)

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Not that I'm aware of. This is on my machine:
none 440G 291G 127G 70% /

Check our docker configuration, maybe you Docker backend has some strange settings? I'm running currently the aufs backend. Docker runs on your host kernel and they are sharing more or less one filesystem.

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My info says - Backing Filesystem: xfs

I have found this on the net:

1. using a different backend (AUFS or BTRFS)
   By starting docker with "-s aufs" or "-s btrfs"

2. using "storage-opt" to increase the devicemapper default size
   By starting docker with "--storage-opt dm.basesize=50G"

if you are AUFS probably I have to see how to do this option?

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The 20 terabytes you're giving to docker goes to /export, not /. As @bgruening said, just change where the tmp directory variables are pointing to so the tool puts things elsewhere. We also commonly use files of that size or larger, but we use FTP to transfer them, which stores things under /export.

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Do you know how to change where the tmp directory variables are pointing to so the tool puts things elsewhere? I'm not aware where this tmp is or how to do that?

Many thanks for the help!!!

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Try changin the new_file_path variable in galaxy.ini, that might do it.

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Sorry for asking but in /export/galaxy-central/config/
I have only these below and no galaxy.ini?
galaxy.ini.docker_sample
galaxy.ini.sample

(creating galaxy.ini from galaxy.ini.docker_sample, editing it, and restarting galaxy did't make any change)

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This should work, but you can always overwrite all variables in galaxy.ini with environment variables ... like described in https://github.com/bgruening/docker-galaxy-stable#galaxys-config-settings

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@ve379 can we close this bug?

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Yes,
I managed the issue just by adding in docker.service
-s devicemapper --storage-opt dm.basesize=20G

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Great! Enjoy Galaxy!

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