reference in builds.txt

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reference in builds.txt

Sabrina rodriguez
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,

Sabrina
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Re: reference in builds.txt

Hans-Rudolf Hotz
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,
>
> Sabrina
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: reference in builds.txt

Hans-Rudolf Hotz
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,
>>>
>>> Sabrina
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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