Hello Sachit,
There are a few problems with the command line. If you want to install
hg19, then hg16 should not be used. Also, the reference_in to the tool
should be an uncompressed fasta file. This is described in the tool
documentation.
You will also need to use as the 'index_basename' the same dbkey
identifier for the genome as you are using to name the reference fasta
file (minus the .fasta extension) and for the SAM index. This is also
the same dbkey identifier as used in the
$GALAXYROOT/tool-data/shared/ucsc/builds.txt file. Using simply hg19
as the dbkey would be the simplest choice.
The original link I sent you explains this, but perhaps you did not find
the data integration wiki page linked from the top? It is important to
know about, as it also covers the builds.txt file in the first section.
It can be found here:
http://wiki.galaxyproject.org/Admin/Data%20Integration
You may find it helpful to rsync the current hg19 genome and indexes
from our server to help you get started. These could be used as a base
from where bowtie2 indexes could be added. Please note that some
genomes, including hg19, have variants in our data archives and that
this particular genome is very large with many indexes and related files
(just a warning if space is a concern). The tool forms for the RNA-seq
tools describe variant content, but in short, the full genome is the
same as the original. It is important to follow the symbolic links to
note which datasets are associated with which indexes and to follow the
same conventions when adding new data. Or take what you need and
reorganize is as it makes the most sense for your own use. This is not
overly complicated - you will be able to see which are associated by
browsing the contained data. The second section on the data integration
wiki page above describes how to rsync, if you choose to do this.
To use the data, even rsync data, the loc files must still be set up.
You only have to set up the ones that you plan to use. The original wiki
link and the one above have information about .loc files, as do the
sample .loc files themselves.
Hopefully this helps,
Jen
Galaxy team
On 12/12/12 9:56 PM, Sachit Adhikari wrote:
I need to install hg19 not hg16.
On Thu, Dec 13, 2012 at 4:26 AM, Sachit Adhikari
sachit.techner...@gmail.com mailto:sachit.techner...@gmail.com wrote:
Hello Jen,
Thanks for your reply. I have installed bowtie2 and tophat2. I am
trying to use this command to build the index:
bowtie2-build [options]* reference_in index_basename
My file name is Homo_sapiens_UCSC_hg19.tar.gz. Thus I used
bowtie2-build -f Homo_sapiens_UCSC_hg19.tar.gz hg16
But it doesn't work. What am I doing wrong? Thanks
On Wed, Dec 12, 2012 at 9:23 PM, Jennifer Jackson j...@bx.psu.edu
mailto:j...@bx.psu.edu wrote:
Hello Sachit,
Instructions for setting up local indexes are in our wiki here:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
Bowtie2 is not specifically listed, but the instructions for
Bowtie and Bowtie2 are nearly identical. The same indexes are
used for Bowtie2 and Tophat2. When building the index, you
simply replace bowtie-build with bowtie2-build in the
command string and create/modify the bowtie2_index.loc file
the same as you would the bowtie_index.loc file.
The Tophat2 manual has some more details about getting set up
here:
http://tophat.cbcb.umd.edu/manual.html
Next time, for questions about local installs, using just the
galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu list is
best (no need to post to multiple lists). If your question has
been misunderstood, please send more details to clarify.
Best,
Jen
Galaxy team
On 12/12/12 3:46 AM, Sachit Adhikari wrote:
How do I add hg16 into the build-in index?
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Jennifer Jackson
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Jennifer Jackson
http://galaxyproject.org
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