I am trying to replicate a RNA-seq analysis done by another institute. I've obtained their data and the Galaxy workflow but am having trouble with four of the tools present in their workflow as Galaxy is not recognizing them. All 4 tools reference the toolshed.g2.bx.psu.edu/repos/devteam/
Ad 1 & 2:
- I'v found the following website that shows 1 and 2 have been removed at some point: https://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=3d4f1fa26f0e&id=c45d6c51a4fcfc6c
- I did a search and found tools 1 & 2 but in a different toolshed: testtoolshed.g2.bx.psu.edu/repos/pavgi/pavgi_picard/ --> I could install the tools from here but the question remains - is this the exact same tool that was used by the other institute?
I am unable to locate this tool, nor identify a possible replacement with a new name
I think this tool has been replaced with "htseq-count" at some point in time -- see website toolshed.g2.bx.psu.edu/lparsons which is also a different toolshed repo than referenced in the workflow and could thus possibly be different.
My question is, where can I locate these older tools to exactly replicate the analysis? I know that Galaxy is strong on reproducibility and with the workflows and detailed history, all steps/tools/versions/parameters etc are well tracked. But it's not easy to exactly replicate a workflow when older tool versions are removed/hidden.
Thank you very much