Data files for FunDO tool in Human Genome Variation?
Hi, I'm trying to get the HGV tools set up on our local instance, and I've hit a stumbling block. I can't find where to get a copy of the data files that FunDO uses. They must exist because the tool seems to work fine on the main PSU instance, but after scouring the project's web page and online supplementary material for the related publications, I'm still empty handed. Anyone know where to obtain them? Is it required to build them again locally? Thanks, Eric
Hi Eric, Yes, you would need the data files locally, sort of the same way that genomes need to be built locally from 3rd party sources. For this dataset, do the following: 1. Obtain the input source data. There are two files. File A. From the downloads section of FunDo website: http://django.nubic.northwestern.edu/fundo/media/data/do_lite.txt The file is tab-separated text. Disease, Entrez gene acc., gene symbol File B. From the UCSC Table browser using "Get Data -> UCSC Main (or from their Downloads website): Genes track including positions, gene acc., and gene symbol. 2. Create a file that is tab-separated text with these columns (correct order is important). chromosome start end strand gene symbol gene acc disease 3. General path to get from 1 -> 2 Sort both of the files by gene accession. Do a join on the accession. Extract the columns used by the tool. You could do #3 in Galaxy with the Text Manipulation tools or outside of Galaxy with unix shell commands or simple scripting, this is up to you. Hopefully this helps! Thank you for you patience, Best, Jen Galaxy team On 1/12/12 9:00 AM, Paniagua, Eric wrote:
Hi,
I'm trying to get the HGV tools set up on our local instance, and I've hit a stumbling block. I can't find where to get a copy of the data files that FunDO uses. They must exist because the tool seems to work fine on the main PSU instance, but after scouring the project's web page and online supplementary material for the related publications, I'm still empty handed.
Anyone know where to obtain them? Is it required to build them again locally?
Thanks, Eric
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Thank you, Jennifer, your reply is much appreciated. I'll try out your instructions and see how this goes today. Best, Eric ________________________________________ From: Jennifer Jackson [jen@bx.psu.edu] Sent: Tuesday, January 17, 2012 6:28 PM To: Paniagua, Eric Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Data files for FunDO tool in Human Genome Variation? Hi Eric, Yes, you would need the data files locally, sort of the same way that genomes need to be built locally from 3rd party sources. For this dataset, do the following: 1. Obtain the input source data. There are two files. File A. From the downloads section of FunDo website: http://django.nubic.northwestern.edu/fundo/media/data/do_lite.txt The file is tab-separated text. Disease, Entrez gene acc., gene symbol File B. From the UCSC Table browser using "Get Data -> UCSC Main (or from their Downloads website): Genes track including positions, gene acc., and gene symbol. 2. Create a file that is tab-separated text with these columns (correct order is important). chromosome start end strand gene symbol gene acc disease 3. General path to get from 1 -> 2 Sort both of the files by gene accession. Do a join on the accession. Extract the columns used by the tool. You could do #3 in Galaxy with the Text Manipulation tools or outside of Galaxy with unix shell commands or simple scripting, this is up to you. Hopefully this helps! Thank you for you patience, Best, Jen Galaxy team On 1/12/12 9:00 AM, Paniagua, Eric wrote:
Hi,
I'm trying to get the HGV tools set up on our local instance, and I've hit a stumbling block. I can't find where to get a copy of the data files that FunDO uses. They must exist because the tool seems to work fine on the main PSU instance, but after scouring the project's web page and online supplementary material for the related publications, I'm still empty handed.
Anyone know where to obtain them? Is it required to build them again locally?
Thanks, Eric
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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Jennifer Jackson -
Paniagua, Eric