Hi Dave,

I can confirm that it is also working for me.

uname -a
Linux threonin 3.5.0-36-generic #57-Ubuntu SMP Wed Jun 19 15:10:49 UTC
2013 x86_64 x86_64 x86_64 GNU/Linux
bag@threonin:~/projects/github/galaxytools$ arch
x86_64
bag@threonin:~/projects/github/galaxytools$ echo $0
bash

Is the toolshed somehow running in chroot or so?
Dave can you grep through the log file and can have a look why the
dependency shell is not build correctly?

Thanks,
Bjoern


> Peter,
> 
> I apologize for the delay, here is the information you requested:
> 
> ubuntu@ip-10-0-0-243:~$ uname -a
> Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 
> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> ubuntu@ip-10-0-0-243:~$ arch
> x86_64
> ubuntu@ip-10-0-0-243:~$ echo $0
> -bash
> 
>     --Dave B.
> 
> On 08/26/2013 09:44 AM, Peter Cock wrote:
> > (Off list)
> >
> > Hi Dave, Greg,
> >
> > Just a reminder - without a bit more information about the Tool Shed
> > cluster I am stuck about how to debug this install issue.
> >
> > Thanks,
> >
> > Peter
> >
> >
> > On Wed, Aug 21, 2013 at 2:05 PM, Peter Cock <p.j.a.c...@googlemail.com> 
> > wrote:
> >> On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
> >>> Peter,
> >>>
> >>> Here is the relevant log output for the installation of ncbi_blast_plus. A
> >>> quick google informs me that exit code 64 means "command line usage 
> >>> error",
> >>> for what it's worth.
> >>>
> >>> ...
> >>> tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new 
> >>> row
> >>> (or updating an existing row) for repository 'package_blast_plus_2_2_26' 
> >>> in
> >>> the tool_shed_repository table, status set to 'New'.
> >>>
> >>> Warning: local() encountered an error (return code 64) while executing '
> >>>                      if [[ "$(uname)" == "Linux" ]]; then export
> >>> FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi &&
> >>>                      if [[ "$(arch)" == "x86_64" ]]; then export
> >>> FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi &&
> >>>                      if [[ "$(uname)" == "Darwin" ]]; then export
> >>> FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi &&
> >>>                      echo Fetching $FILENAME &&
> >>>                      if [[ "$(uname)" == "Linux" ]]; then wget
> >>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi 
> >>> &&
> >>>                      if [[ "$(uname)" == "Darwin" ]]; then curl -O
> >>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi 
> >>> &&
> >>>                      tar -zxvf $FILENAME &&
> >>>                      echo Downloaded and decompressed
> >>>                  '
> >>>
> >>
> >> Thanks Dave,
> >>
> >> I've made a note on this Trello card about exposing the log information
> >> of unsuccessful builds on the Tool Shed,
> >> https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages
> >>
> >> Can you tell me what version of Linux this is, and which shell?
> >>
> >> $ uname
> >> ...
> >>
> >> $ arch
> >> ...
> >>
> >> $ echo $0
> >> ...
> >>
> >> That might give me a clue about the nature of the failure. My
> >> hunch is that I am using something bash specific.
> >>
> >> The simplest solution would be if you could run each of these
> >> command by hand to see if it triggers the same error:
> >>
> >> if [[ "$(uname)" == "Linux" ]]; then export 
> >> FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi
> >> if [[ "$(arch)" == "x86_64" ]]; then export 
> >> FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi
> >> if [[ "$(uname)" == "Darwin" ]]; then export 
> >> FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi
> >> echo Fetching $FILENAME
> >> if [[ "$(uname)" == "Linux" ]]; then wget 
> >> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
> >> if [[ "$(uname)" == "Darwin" ]]; then curl -O 
> >> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi
> >> tar -zxvf $FILENAME
> >> echo Downloaded and decompressed
> >>
> >> Thanks,
> >>
> >> Peter



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