Yeah - I am with you on this. It is definitely less than ideal that any exception will cause that to happen.
Here is a commit that I believe should fix the problem: https://github.com/galaxyproject/galaxy/commit/87e19aa4d708d6c719b396867f431d94c92077c5 Do you have a working run-as-real user setup to test this - it would take some time for me to test this but if you have something ready to go - let me know and I will open a PR :). Also - I noticed the documentation for the run-as-real-user stuff seems to match the code implementation - can you peak at https://github.com/galaxyproject/galaxy/pull/94 and let me know if it more accurately reflects how you got things up and running? Thanks for finding and reporting this issue! -John On Mon, Mar 30, 2015 at 3:33 PM, David Trudgian < david.trudg...@utsouthwestern.edu> wrote: > Hi, > > > > Looking through the DRMAA job runner code I noticed that in > lib/galaxy/jobs/__init__.py:1582 that if chown to a user in > change_ownership_for_run fails then there is chmod 0777 instead. > > > > I’m thinking that this probably shouldn’t happen by default, or there > needs to be a big warning on the wiki? I understand the world-readable > security concerns posted there – but world-writable, for whatever reason, > on a shared cluster seems like a disaster waiting to happen. > > > > Maybe either warn on the wiki, make the chmod 777 a non-default option, or > an option to disable it? > > > > DT > > ------------------------------ > > UT Southwestern > > Medical Center > > The future of medicine, today. > > ___________________________________________________________ > 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/mailinglists/ >
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