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.c...@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-packages
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
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