Am Montag, den 07.10.2013, 10:36 -0500 schrieb John Chilton: > On Mon, Oct 7, 2013 at 10:22 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > > On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock <p.j.a.c...@googlemail.com> > > wrote: > >> On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier <d...@bx.psu.edu> wrote: > >>> Peter, > >>> > >>> I did some investigating, and it turns out that the if [[ condition ]] > >>> syntax used in the ncbi tool dependency is only compatible with bash, not > >>> sh. > >> > >> Does that mean the test system has switched between sh and bash > >> and back to sh again? > > > > Is there anything written down about the expected shell(s) > > available for a standard Galaxy instance? > > I don't think it is documented anywhere and there has been some > disagreement on this in the past. I think we should do our best to > reach some sort of conclusion on this and document it in the following > card: > > https://trello.com/c/7VTlX9rD > > My own preference is that we specify at least /bin/sh and /bin/bash > are available before utilizing the tool shed. Is there an objection to > this from any corner? Is there realistically a system that Galaxy > should support that will not have /bin/bash available? I know there is > some difference in bash behavior between platforms, but that is > hopefully minimal and we can address inconsistencies one at a time.
I think we can and should assume /bin/bash on every system. We also should finally write down the dependency list. We talked a lot about it and we collected a lot of system libraries and dependencies the TS and all tools can depend on. We just need to write it down. I will comment on that trello card! Bjoern > Thanks, > -John > > > > >>> For sh, the corresponding syntax would look like: > >>> > >>> if [ "$string" = "value" ] > >>> then > >>> echo "string is equal to value" > >>> fi > >>> > >>> However, it strikes me that the platform detection and download url > >>> determination could also be done using the recently introduced > >>> <actions_group> feature, which would bypass shell-dependent > >>> conditional syntax entirely. > >> > >> Yes, but is that in stable releases for galaxy-dist yet? > > > > In the meantime I will try that on the Test Tool Shed, based > > on the tool_dependencies.xml example you shared before: > > > > http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26/c83440a9bdfb > > > > Note there seems to me to be a lot of duplication - I would like > > a way to unambiguously combine multiple CPU architectures > > into a single action. > > > > For example, combine these: > > > > <actions os="darwin" architecture="x86_64"> > > <actions os="darwin" architecture="i386"> > > > > into: > > > > <actions os="darwin" architecture="x86_64,i386"> > > > > or just: > > > > <actions os="darwin"> > > > > and similarly, combine these: > > > > <actions os="linux" architecture="i386"> > > <actions os="linux" architecture="i686"> > > > > into something like: > > > > <actions os="linux" architecture="i386,i686"> > > > > Assuming that works on the Test Tool Shed, and the code for > > this is already in the stable releases, I will update the main > > Tool Shed definition as well. > > > > Thanks, > > > > Peter > > ___________________________________________________________ > > 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: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
