docker folder permissions on Mac

[claymcleod]

Hey @mlin,

I got the following error when I did miniwdl run_self_test: wondering if you have ever seen it before? I haven't had a chance to dive in an look, probably can do so tonight but wanted to get your thoughts if you have run into it before.

2020-01-19 16:23:47,191 miniwdl-run ERROR task hello (/var/folders/z9/7n3_5hks21s7d1bz5ppx2zqxx4ymd8/T/miniwdl_run_self_test_fvg99d4e/test.wdl Ln 17 Col 13) failed
2020-01-19 16:23:47,191 miniwdl-run ERROR RuntimeError, docker task rejected: invalid mount config for type "bind": bind source path does not exist: /var/folders/z9/7n3_5hks21s7d1bz5ppx2zqxx4ymd8/T/miniwdl_run_self_test_fvg99d4e/20200119_162345_hello_caller/write_/tmpn181hh6p

For the record, docker is configured to work with my non-root user, though I don't think that's the issue:

 cmcleod@x86_64-apple-darwin13  ~/Desktop/ngsderive  docker ps                                                                              1 ↵  7692  16:23:47
CONTAINER ID        IMAGE                                 COMMAND                  CREATED             STATUS              PORTS                               NAMES
d725e8b8bd94        postgres                              "docker-entrypoint.s…"   2 months ago        Up 3 days           5432/tcp, 0.0.0.0:54320->5342/tcp   vis_postgres_1

[mlin]

Gotta set TMPDIR on MacOSX...we need to add a warning msg about this. See: common-workflow-language/cwltool#328

…

Sent from my iPhone

On Jan 19, 2020, at 12:26, Clay McLeod ***@***.***> wrote:  Hey @mlin, I got the following error when I did miniwdl run_self_test: wondering if you have ever seen it before? I haven't had a chance to dive in an look, probably can do so tonight but wanted to get your thoughts if you have run into it before. 2020-01-19 16:23:47,191 miniwdl-run ERROR RuntimeError, docker task rejected: invalid mount config for type "bind": bind source path does not exist: /var/folders/z9/7n3_5hks21s7d1bz5ppx2zqxx4ymd8/T/miniwdl_run_self_test_fvg99d4e/20200119_162345_hello_caller/write_/tmpn181hh6p``` For the record, `docker` is configured to work with my non-root user, though I don't think that's the issue: ***@***.***_64-apple-darwin13  ~/Desktop/ngsderive  docker ps  1 ↵  7692  16:23:47 CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES d725e8b8bd94 postgres "docker-entrypoint.s…" 2 months ago Up 3 days 5432/tcp, 0.0.0.0:54320->5342/tcp vis_postgres_1 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[claymcleod]

Great, that fixed it. I can throw together a PR, were you thinking just a docs update or an actual warning shown by the CLI (or both)?

…

On Jan 19, 2020, at 7:36 PM, Mike Lin ***@***.***> wrote: Gotta set TMPDIR on MacOSX...we need to add a warning msg about this. See: common-workflow-language/cwltool#328 Sent from my iPhone > On Jan 19, 2020, at 12:26, Clay McLeod ***@***.***> wrote: > >  > Hey @mlin, > > I got the following error when I did miniwdl run_self_test: wondering if you have ever seen it before? I haven't had a chance to dive in an look, probably can do so tonight but wanted to get your thoughts if you have run into it before. > > 2020-01-19 16:23:47,191 miniwdl-run ERROR RuntimeError, docker task rejected: invalid mount config for type "bind": bind source path does not exist: /var/folders/z9/7n3_5hks21s7d1bz5ppx2zqxx4ymd8/T/miniwdl_run_self_test_fvg99d4e/20200119_162345_hello_caller/write_/tmpn181hh6p``` > > For the record, `docker` is configured to work with my non-root user, though I don't think that's the issue: > > ***@***.***_64-apple-darwin13  ~/Desktop/ngsderive  docker ps  1 ↵  7692  16:23:47 > CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES > d725e8b8bd94 postgres "docker-entrypoint.s…" 2 months ago Up 3 days 5432/tcp, 0.0.0.0:54320->5342/tcp vis_postgres_1 > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub, or unsubscribe. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[mlin]

I'm thinking that if miniwdl run_self_test fails, it should determine if (i) current platform is Mac and (ii) TMPDIR is under /var. If so, print a message something like "Hint: try export TMPDIR=/tmp prior to miniwdl; more info https://...". This should appear toward the end of the standard error log to ensure it's visible on the user's terminal.

I don't have access to a Mac right now, probably will soon but help in the meantime would definitely be appreciated!

[mlin]

Added the warning and consolidated other macOS-related issues in #145