Peter, Our approach has always been to treat each tool shed repository as a self-contained entity. This means that all required components are contained in the repository or definitions for obtaining them from remote repositories are contained in the repository. You'll notice that several tools that have been migrated to the tool shed from the distribution have 1.bed in their test-data directory. Our reasoning for that approach is that in the unlikely event that the distribution's version of 1.bed is changed, the repository version will still be valid for that repository's tool functional tests. Additionally, Ssuis.fasta may eventually be migrated out of the distribution, in which case any repository installed from the tool shed that depends on Ssuis.fasta will fail functional tests. However, I see your point about the file size, 1.9MB is a bit substantial for a test file. Is it possible to rewrite the test to use a smaller file? --Dave B. On 4/23/13 10:25:38.000, Peter Cock wrote:

Hi Greg/Dave,

I've noticed an oddity with another unit test failure on the main Tool Shed,

http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss Revision: 1:922d69bd5258 Tool id: get_orfs_or_cdss version: 0.0.2 Reason test is invalid One or more test files are missing for tool get_orfs_or_cdss: Ssuis.fasta

The tool tests should be failing as they are omitting some test files, which I'd not included in the uploaded tar ball (I'll fix this shortly):

test-data/get_orf_input.fasta test-data/get_orf_input.Suis_ORF.nuc.fasta test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.t11_nuc_out.fasta test-data/get_orf_input.t11_open_nuc_out.fasta test-data/get_orf_input.t11_open_prot_out.fasta test-data/get_orf_input.t11_prot_out.fasta test-data/get_orf_input.t1_nuc_out.fasta test-data/get_orf_input.t1_prot_out.fasta

However, I believe the ToolShed warning is misleading as test-data/Ssuis.fasta is already present as part of the Galaxy core install. This is why I have used it (and other bundled files like it) to minimise the download size of the tool itself.

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/

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