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 $0 -bash
--Dave B.
On 08/26/2013 09:44 AM, Peter Cock wrote:
(Off list)
Hi Dave, Greg,
Just a reminder - without a bit more information about the Tool Shed cluster I am stuck about how to debug this install issue.
Thanks,
Peter
On Wed, Aug 21, 2013 at 2:05 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
Here is the relevant log output for the installation of ncbi_blast_plus. A quick google informs me that exit code 64 means "command line usage error", for what it's worth.
... tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new row (or updating an existing row) for repository 'package_blast_plus_2_2_26' in the tool_shed_repository table, status set to 'New'.
Warning: local() encountered an error (return code 64) while executing ' if [[ "$(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-pac...
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