Hi,
imported from usegalaxy.org workflow CloudMap_Hawaiian_Variant_Mapping_with_WGS to local Galaxy instance (16.04) shows missing tools or their different versions.
For instance: *Tool name* Add or Replace Groups, *id* toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0, *version* 1.56.0 *Tool name* Mark Duplicate reads, *id* toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0, *version* 1.56.0 Also it requires SNP 1.56 version.
Our Galaxy instance has the latest tools version for 16.04. Does it mean I have to install older version of tools or modify workflow to use latest one? (As I see workflow asks for programs with different ids what was in older versions: picard_ARRG in 1.56 but it probably is already picard_AddOrReplaceReadGroups in 1.136. Or bedtools from aaronquinlan repository with id="bedtools_genomecoveragebed_bedgraph" and which is not available in 16.04 repositories but probably this program is in bedtools from iuc with id="bedtools_genomecoveragebed"). Also I see that tools on usegalaxy.org are even newer than our but this workflow is imported there without any errors. Does it mean that on usegalaxy.org there are many versions of the same tool but they are not visible in tools panel?
Does some one have modified version of this workflow (or similar to try just cloudmap tests) to new Galaxy instance?
Thanx, Nikolaos