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. 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. --Dave B. On 10/07/2013 09:45 AM, Peter Cock wrote:
On Tue, Sep 24, 2013 at 10:58 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
Some good news, the strange missing /bin/sh error has gone away on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/aecdffbc08fc
The BLAST+ wrapper tests also look good on the main Tool Shed:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus /70e7dcbf6573
Hooray!
Peter
P.S. Another plug for explicitly testing Tool Dependency Definition package installation on the Tool Shed: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-pac...
Bad news, the strange missing /bin/sh error has come back again on both the main and Test Tool Shed :(
These are the same revisions of the BLAST+ wrapper, so the only changes are in Galaxy itself, the Tool Shed itself, or the Tool Shed test environment:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/aecdffbc08fc http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus /70e7dcbf6573
Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion blast+ package 2.2.26+ Error /bin/sh: 2: [[: not found /bin/sh: 3: [[: not found /bin/sh: 4: [[: not found /bin/sh: 6: [[: not found /bin/sh: 7: [[: not found tar: option requires an argument -- 'f' Try `tar --help' or `tar --usage' for more information.
Regards,
Peter