I installed a local instance of GALAXY following the instructions at "Get
Galaxy ..." in the Wiki. It installed ok, but when I tried the Bowtie2 mapper
with a test data set, I noticed that the reference genomes are missing. How can
I get the reference genomes (e.g. latest version of mouse and hu
Here are a couple of questions on rsync:
1. the amount of files for hg19 and mm9 is extremely different (over 600 vs. 88
Gb) - why is that so?
2. if I list the directories for hg19 and mm9, there seems to be a group of
files for bowtie2 in hg19, but not in mm9 - where are the ones for mm9?
3. g
Here are a couple of questions on rsync:
1. the amount of files for hg19 and mm9 is extremely different (over 600 vs. 88
Gb) - why is that so? They are both mammalian genomes ... are there redundant
files in hg19, is mm9 incomplete...?
2. if I list the directories for hg19 and mm9, there seems t
Trying out a local instance of Galaxy. Small files can be uploaded with
"browse.." but this works only for files under 2Gb. Is there a folder in a
local copy of galaxy-dist where I can copy a large file and have it show up in
the Get Data/Upload File/Files uploaded via FTP window so that I can p
I'll leave the rsync question to the experts - worked for me, but I don't know
why it worked for me (linux/ubuntu laptop, not networked) and not for you .
About the filenames: You can download a file listing to text.txt by
.../galaxy-dist$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes >
Can I put in a similar question on top of this: How much resources do you need
for re-sequencing of a mammalian genome (assembly and variant detection), one
job at a time? E.g. how much RAM etc. if I want the re-sequencing SAM file of
a 30-fold coverage be done in 48 hours?
Gerald
Gerald
(one single lab) or a production instance (whole
institute or more) would be great
... or could anybody give their own 2 cents?
Gerald
>
> From: Jeremy Goecks
>To: Gerald Bothe
>Cc: Nikos Sidiropoulos ; Peter Cock
>; ""
>Sent
