Hi Curtis,
This is still open but I expect to correct this very soon, along with new data additions (but corrections first on the list!). We definately consider this important and apologize that this has impacted your paper's supplemental creation.


There is a Trello ticket containing the known data problems since the migration of usegalaxy.org, you can follow for updates here: https://trello.com/c/SbizUDQt

Thanks!

Jen
Galaxy team

On 10/29/13 8:18 AM, Curtis Hendrickson (Campus) wrote:

Jennifer,

What's the status of bowtie2/mm9 index on PSU main?

When I select tophat2, it offers me mm9 as a choice for built-in indexes.

However, when the job runs, I get the following error, indicating the bowtie2/mm9 indexes are missing (below).

Any insight into whether this is expected, or what the ETA is until the index would be installed, would be great.

I'm trying to reproduce work on PSU I ran on my local galaxy, so that we can link to it for supplemental materials for a paper.

Thanks,

Curtis

PS -- I clicked the submit bug button a few days ago, but haven't received a response yet.

Fatal error: Tool execution failed

[2013-10-29 10:13:27] Beginning TopHat run (v2.0.9)

-----------------------------------------------

[2013-10-29 10:13:27] Checking for Bowtie

                   Bowtie version: 2.1.0.0

[2013-10-29 10:13:27] Checking for Samtools

                 Samtools version: 0.1.18.0

[2013-10-29 10:13:27] Checking for Bowtie index files (genome)..

Error: Could not find Bowtie 2 index files (/galaxy/data/mm9/mm9full/bowtie2_index/mm9full.*.bt2)

*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Friday, September 20, 2013 4:00 PM
*To:* Curtis Hendrickson (Campus)
*Subject:* Re: [galaxy-dev] datacache & bowtie2 for mm9 ?

Thanks Curtis,

I am actually working to try to get mm9 out there right now. No promises, but is just one (well, three, including variants)! If technical is a go, then will do it. Ideally others soonish. We'll see.

The last news brief has help for the Data manager, it may be that you need to do some config changes to get it going. I am certainly no expert - this is Dan's and under active development - but is where I would start.

Jen

On 9/20/13 1:25 PM, Curtis Hendrickson (Campus) wrote:

    Thanks for the rapid reply! I have some questions and comments,
    but need to read up on Data Managers (that admin page seems
    non-functional in our local galaxy, despite being on latest code)
    first.

    Regards,

    Curtis

    *From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
    *Sent:* Friday, September 20, 2013 2:34 PM
    *To:* Curtis Hendrickson (Campus)
    *Cc:* galaxy-...@bx.psu.edu <mailto:galaxy-...@bx.psu.edu>
    *Subject:* Re: [galaxy-dev] datacache & bowtie2 for mm9 ?

    Hello Curtis,

    The datacache was originally pointed to the data staging area and
    is now pointed to the data published area. The difference is that
    the published area contains data and location (.loc) files that
    are in synch and have completed final testing. It is your choice
    about whether to use the staged-only data - it depends how risk
    tolerant your project is and if you plan on testing. But, that
    said, I think it is almost certainly fine or our team wouldn't
    have staged it yet. A vanishingly small number of datasets are
    pulled back once they make it to staging, and this is why we were
    comfortable pointing datacache there in the first place (were
    unable to point to the published area at first, but wanted to make
    the data available ASAP).

    Going forward - I can let you know that these indexes are very
    easy to create: one command-line execution, then add one line to
    the associated .loc file. Instructions are here, see "Bowtie and
    Tophat":
    http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

    For one or few genomes, not a problem. For hundreds of genomes
    with variants, can become tedious even with helper tools and in
    our case, the processing interacted with disk that was undergoing
    changes (as we have been working on system configuration most of
    the summer). Also, with the Data Manager is now available,
    creating batch indexes for use via rsync become lower priority.
    Even so, I would expect more indexes to be fully published once
    the final configuration is in place, as many are already staged or
    close being staged (watch the yellow banner on Main).

    Hopefully this helps to explain the data, guides you to making an
    informed decision, and aids with creating your own indexes as needed,

    Thanks!
    Jen
    Galaxy team



    On 9/18/13 1:04 PM, Curtis Hendrickson (Campus) wrote:

        Folks,

        First, I wanted to thank you for making the datacache
        available
        (http://wiki.galaxyproject.org/Admin/Data%20Integration;
        rsync://datacache.g2.bx.psu.edu). It's a great resource.

        However, what is the best way to stay abreast of changes to
        what's in datacache, and understand how these indexes are
        computed?

        We are currently upgrading to bowtie2, but I notice that the
        bowtie2 indices for mm9, which used to be in

        rsync://datacache.g2.bx.psu.edu/indexes/mm9/mm9*/bowtie2_index

        have been removed, and only the hg19 genome has bowtie2
        indices. Why only that one, and not the others?

        Where are the scripts you use to make these indices, in case I
        want to create bowtie2 indices for other

        So, how do I find out **why** they were removed? (Can I safely
        use the copy I have, or was there a problem with them?)

        More generally, how do I understand the policies and logic
        behind the datacache indices, and be notified of changes,
        short of running my own periodic rsync/diff?

        Finally, since I'm doing "reproducible research" is anything
        planned for systematically versioning genome indices, so I can
        easily tell what version of a system (ie, what BWA version)
        was used to create the index, and be sure that an index will
        not suddenly disappear.


        Thanks,

        Curtis

        Research Associate/CTSA-Informatics Team

        University of Alabama at Birmingham





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--
    Jennifer Hillman-Jackson

    http://galaxyproject.org



--
Jennifer Hillman-Jackson
http://galaxyproject.org

--
Jennifer Hillman-Jackson
http://galaxyproject.org

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