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.
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.
Next time, for questions about local installs,
using just the galaxy-dev@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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