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.technerves@gmail.com <mailto:sachit.technerves@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 <jen@bx.psu.edu <mailto:jen@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-dev@bx.psu.edu <mailto: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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