Re: [galaxy-dev] package_bowtie_2_2_4 Executable Permissions - can't run bowtie as non-galaxy user
Hi David, can you open an issue at https://github.com/galaxyproject/docker-build ? Thanks, Nicola Il 18.06.2015 21:55 David Trudgian ha scritto: > Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4, which downloads bowtie binaries from depot.galaxyproject.org > > http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.4-linux-x86_64.tgz > > Jobs submitted on our setup, running as a 'real user' (not galaxy user) via pulsar + SLURM fail with a permissions error. This is due to the permissions on some of the bowtie executables in the .tar.gz from depot being owner/group executable only. Other users cannot run bowtie2: > > -rwxrwx---. 1 galaxy galaxy 18K Oct 22 2014 bowtie2 > > If I download the tar.gz from depot manually and extract then I get: > > -rwxrwx--- 1 dtrudgian biohpc_admin 18K Oct 22 2014 bowtie2 > > Could the .tar.gz be fixed, so that the executables will work in a run as real user configuration? Is there any sensible way Galaxy could enforce permissions to guard against this issue? > > Cheers, > > -- > > David Trudgian Ph.D. > > Computational Scientist, BioHPC > > UT Southwestern Medical Center > > Dallas, TX 75390-9039 > > Tel: (214) 648-4833 > > Please contact biohpc-help@utsouthwestern with general BioHPC inquries. > > - > > UT Southwestern > > Medical Center > > The future of medicine, today. Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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/
Re: [galaxy-dev] package_bowtie_2_2_4 Executable Permissions - can't run bowtie as non-galaxy user
Hi David, can you open an issue at https://github.com/galaxyproject/docker-build ? Thanks, Nicola Il 18.06.2015 21:55 David Trudgian ha scritto: > Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4, which downloads bowtie binaries from depot.galaxyproject.org > > http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.4-linux-x86_64.tgz > > Jobs submitted on our setup, running as a 'real user' (not galaxy user) via pulsar + SLURM fail with a permissions error. This is due to the permissions on some of the bowtie executables in the .tar.gz from depot being owner/group executable only. Other users cannot run bowtie2: > > -rwxrwx---. 1 galaxy galaxy 18K Oct 22 2014 bowtie2 > > If I download the tar.gz from depot manually and extract then I get: > > -rwxrwx--- 1 dtrudgian biohpc_admin 18K Oct 22 2014 bowtie2 > > Could the .tar.gz be fixed, so that the executables will work in a run as real user configuration? Is there any sensible way Galaxy could enforce permissions to guard against this issue? > > Cheers, > > -- > > David Trudgian Ph.D. > > Computational Scientist, BioHPC > > UT Southwestern Medical Center > > Dallas, TX 75390-9039 > > Tel: (214) 648-4833 > > Please contact biohpc-help@utsouthwestern with general BioHPC inquries. > > - > > UT Southwestern > > Medical Center > > The future of medicine, today. Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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/
[galaxy-dev] package_bowtie_2_2_4 Executable Permissions - can't run bowtie as non-galaxy user
Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4, which downloads bowtie binaries from depot.galaxyproject.org http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.4-linux-x86_64.tgz Jobs submitted on our setup, running as a 'real user' (not galaxy user) via pulsar + SLURM fail with a permissions error. This is due to the permissions on some of the bowtie executables in the .tar.gz from depot being owner/group executable only. Other users cannot run bowtie2: -rwxrwx---. 1 galaxy galaxy 18K Oct 22 2014 bowtie2 If I download the tar.gz from depot manually and extract then I get: -rwxrwx--- 1 dtrudgian biohpc_admin 18K Oct 22 2014 bowtie2 Could the .tar.gz be fixed, so that the executables will work in a run as real user configuration? Is there any sensible way Galaxy could enforce permissions to guard against this issue? Cheers, -- David Trudgian Ph.D. Computational Scientist, BioHPC UT Southwestern Medical Center Dallas, TX 75390-9039 Tel: (214) 648-4833 Please contact biohpc-help@utsouthwestern with general BioHPC inquries. 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/