Hi Sabrina

Always include the mailing list, so others can help and/or learn as well. See my comments below....

On 05/13/2015 09:40 AM, Sabrina rodriguez wrote:

Hi Hans-Rudolf,

Thanks for your answer.

I have made 2 .loc files for indexed genomes for 2 different tools (STAR and tophat) on the same reference genome fasta file (ex: sus crofa).

In tophat.loc, I have: ensembl_sus_scrofa_genome ensembl_sus_scrofa_genome ensembl sus scrofa genome /bank/bowtie2db/ensembl_sus_scrofa_genome

In STAR.loc, I have: STAR-ensembl_sus_scrofa_genome STAR-ensembl_sus_scrofa_genome STAR-ensembl_sus_scrofa_genome /bank/STARdb/STAR-ensembl_sus_scrofa_genome

Since it is the same genome, I would use the same dbkey for both '*loc'files'. Short names for for dbkeys are recomended, eg: 'susScrLX'

In builds.txt, I have: STAR-ensembl_sus_scrofa_genome STAR-ensembl_sus_scrofa_genome (ensembl_sus_scrofa)

I would just add an extra line, similar to the existing one for 'susScr2', eg:

susScrLX local Pig May 2015 (susScrLX) (susScrLX)

The 2 indexed come from the same reference genome.

Once the tools are processed, I need to precise the reference genome using the "pencil" and so using the "builds.txt" information ; because after that I am using a tool that needs the reference genome information (sam-to-bam tool).

Make sure the input data (fastq files I assume) have already the right dbkey. This way, the results (sam files) will inherit the dbkey.

I think I read that the dbkey must be the same as the one from the .loc file.

If the dbkey is unique in builds.txt file, does it mean that I need to create 1 line per tool per reference genome in the builds.txt file?

no, just one per genome, which is then used in the different '*loc' files

How does galaxy know where to find the information from the builds.txt file as in the builds.txt file, no path are indicated?

The information from the "builds.txt" is more like meta data associated with the individual history items, And hence independent of the tools used

Hans-Rudolf

Thanks in advance for your answers.

Best regards,

Sabrina

On 13/05/2015 09:17, Hans-Rudolf Hotz wrote:

...

Hi Sabrina

yes, you can add any genome to "builds.txt" (as an example, we have several plasmids added as genomes in our Galaxy server). Just make sure the dbkey (e.g. hg19) you gonna add is unique.

If you also intend to use the built in visualization tools, make sure to add the corresponding files to "/tool-data/shared/ucsc/chrom/"

And don't forget to restart the server, to put the changes into effect

Hans-Rudolf

On 05/12/2015 05:29 PM, Sabrina rodriguez wrote:

...

Dear all,

I am working on integrating some bioinformatics tools into galaxy for a research team in France. I have a question with regard to the "/tool-data/shared/ucsc/builds.txt" file. I would like to add a new reference genome that is not coming from UCSC. Could you please tell me if this is feasible and, in that case, how to process?

Thank you very much in advance.

Best regards,

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