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where do I find SamToFastq.jar ? [reproducibility?]

zimounzimoun parisMember

Dear Community,

I am from system-administrator side, and totally new in this field about bio-informatic, so excuse my weird question.

I am attempting to reproduce results of:
Nature Biotechnology 33, 1152–1158 (2015) doi:10.1038/nbt.3344
http://archive.broadinstitute.org/cancer/cga/polysolver

The main issue is that they do not provide the exact versions of the used tools, neither git commits.

Now, (at least) 2 years after, it is (unfortunately) almost impossible to re-launch --as-is-- their test-cases and there is some errors, just because the User-Interface of such tools have evolved (hopefully! ;-).
I do not want to re-write and/or adapt polysolver to the current and latest versions of the tools, just re-run the published software.

Well, I have read some Release Notes, trying to identify the versions. But, at some point, it is unfruitful... and too painful!

One of there errors is about GATK, i.e., polysolver claims:
Error: Unable to access jar file path/to/gatk/SamToFastq.jar

Where do I find SamToFastq.jar ?

Does it move to Picard ?
If yes, now it seems that the UI is not SamToFastq.jar but java -jar path/to/picard/picard.jar <tool-name> .... Therefore, what is the last version of Picard considering the previous UI ?

Or maybe, I am not able to correctly read the documentation and I miss a point.

Thank you in advance for any advice !

All the best!

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, what you're looking for is an older version of the Picard toolkit from when the tools where each packaged into separate jars (probably a version 1.x). You can find older releases of Picard here: https://github.com/broadinstitute/picard/releases/. You will have an easier time if you find the exact Picard version they used; it should be listed in the Materials and Methods section of the paper.

  • zimounzimoun parisMember

    Hi,

    Thank you for the details.

    I have already checked the paper, and maybe my eyes are not good enough, but I do not find any reference to any version. Sadly.

    Well, I was hoping that just give a look at some RELEASE files will be enough to find the last older version of this older UI.
    Then, I will try the version 1.x. More than 130 versions... I hope that dichotomy will let me check few versions.

    Thank you again to bound a bit the search process.
    If you remind more information, then let me know.

    All the best!

    ps:
    Yes, it is not an easy time... and I worry about Science and computational tools... for example http://reproducibility.cs.arizona.edu is so ouch! Well, I mention https://www.gnu.org/software/guix/ which especially targets reproducibility tools. Whatever! Another topic...

  • Hi zimoun,
    I wonder if you can see my post now, after 2months.
    I am now using polysolver and have a problem same as you. I find the right picard tools version here https://sourceforge.net/projects/picard/files/picard-tools/
    the version 1.119 is OK.
    You just need to download and unzip the file, then set the GATK_PATH to this directory. The polysolver will successfully run on the example data.
    Hope you can see my post and help you.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited June 2017

    @snoopy448
    Hi,

    Thanks for reporting your solution! It is nice to see the GATK community sharing tips with each other :smile:.

    -Sheila

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