Access to removed tools from Galaxy toolshed

Question: Access to removed tools from Galaxy toolshed

2.9 years ago by

PKL • 0

PKL • 0 wrote:

Hi,

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/

1. picard/rgPicardMarkDups/1.56.0

2. picard/PicardASMetrics/1.56.0

3. picard/PicardRnaSeqMetrics/1.56.0

4. htseq_count/htseq_count/0.4.1

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?

Ad 3:

I am unable to locate this tool, nor identify a possible replacement with a new name

Ad 4:

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.

Please advice.

Thank you very much

rna-seq galaxy • 886 views

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modified 2.9 years ago by Martin Čech ♦♦ 4.9k • written 2.9 years ago by PKL • 0

2.9 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

Repositories never disappear from the Tool Shed, if the author thinks they are not useful anymore they can be deprecated (hidden from default search) but still can be installed. Moreover the picard tools in version 1.56.0 are in the same repository as the new ones, just an older revision (repository revision 4 from 2014-02-21). The htseq_count is made by Lance parsons and the revision you are looking for is 19. I included the links below, please let me know if you need more information

1,2,3: https://toolshed.g2.bx.psu.edu/view/devteam/picard/ab1f60c26526
4: https://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count/6f920f33c5eb

ADD COMMENT • link modified 2.9 years ago • written 2.9 years ago by Martin Čech ♦♦ 4.9k

Thank you very much, Martin. I have 2 remaining questions:

I am happy to learn that the older tool versions are simply hidden. I now see that by searching through the various revisions of the repositories, I can find the older tool versions. Is there actually an easier way to search for a particular tool version within repository versions versus looking at each repository revision's content?

The older tool versions have been installed successfully now, but I don't seem to be able to locate tool number 3 within the 1.56.0 version of picard ("picard/PicardRnaSeqMetrics/1.56.0"). Do you have any thoughts on this?

Thank you again.

ADD REPLY • link written 2.9 years ago by PKL • 0

I think we do not have a better way to search for a particular version of a tool yet. We have an experimental search interface at http://toolshed.tools that will eventually have this ability, but not yet.

That PicardRnaSeqMetrics puzzles me. It seems that this tool did not ever exist in that version on the Main Tool Shed. According to this commit the tool file was added first in the 1.126 picard: https://github.com/galaxyproject/tools-devteam/commit/44c38d9cf950b5c42f5229077437061cd47d0649#diff-9979375df6651b5afefa5d66f28bf539R1

Can you please double check that you were using this specific version?

ADD REPLY • link modified 2.9 years ago • written 2.9 years ago by Martin Čech ♦♦ 4.9k

The workflow I have received indeed lists this tool in this specific version. Here's a copy straight from the workflow:

Step 12: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardRnaSeqMetrics/1.56.0'

ADD REPLY • link written 2.9 years ago by PKL • 0

that is very interesting, the rnaseqmetrics tool has this id: picard_CollectRnaSeqMetrics (different from that one you shared)

can you please share the whole workflow with me? (e.g. using gist.github.com )

ADD REPLY • link modified 2.9 years ago • written 2.9 years ago by Martin Čech ♦♦ 4.9k

Martin -- you can find the workflow at: https://gist.github.com/plebeau/8380a8804df21462cf5d

ADD REPLY • link modified 2.9 years ago • written 2.9 years ago by PKL • 0

Dan Blankenberg did some detective work and found the tool of the given version and id in a patch on our issue tracker here: https://trello.com/c/rLAIL0vY/1465-add-rna-seq-metrics-and-downsample-sam-to-picard-tools

This patch has never made it to the Tool Shed.

So our theory right now is that the Galaxy that exported your workflow had somehow this patch manually applied. Do you know which Galaxy is this workflow exported form?

ADD REPLY • link modified 2.9 years ago • written 2.9 years ago by Martin Čech ♦♦ 4.9k

Thank you Martin and Dan - great detective work. I'll ask the other institution and get back with you as soon as I have an answer.

ADD REPLY • link written 2.9 years ago by PKL • 0

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