Hi Nikolaos,

you may want to take a look at MiModD (www.celegans.de), our new tool suite for mapping-by-sequencing analyses, as a simple and modern replacement for CloudMap. It offers all the functionality of CloudMap, but is more flexible in the types of analyses it can perform and has much simpler workflows.


Of course, others here may want to say more about your actual CloudMap dependencies issue.

Best,
Wolfgang


On 26.06.2016 14:53, Nikolaos Tur wrote:
Hi,

imported from usegalaxy.org <http://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
<http://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
<http://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 <http://usegalaxy.org> are even
newer than our but this workflow is imported there without any errors.
Does it mean that on usegalaxy.org <http://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



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