Hi Moritz,

Pls see below

On Jul 26, 2013, at 6:37 AM, Moritz Juchler <juch...@stud.uni-heidelberg.de> 
wrote:

> Hey,
> 
> 1 I installed Galaxy locally.
> 2 I also have BWA installed and then used the 
> 3 shed repository to get the bwa wrapper.
> 4 I have the reference genome:
>> -rw-r--r-- 1 trr users      10509 2013-07-25 11:31 human_g1k_v37.dict
>> -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta
>> -rw-r--r-- 1 trr users       6597 2013-07-25 19:41 human_g1k_v37.fasta.amb
>> -rw-r--r-- 1 trr users       6844 2013-07-25 19:41 human_g1k_v37.fasta.ann
>> -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt
>> -rw-r--r-- 1 trr users       2746 2013-07-25 11:32 human_g1k_v37.fasta.fai
>> -rw-r--r-- 1 trr users  775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac
>> -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa
>  
> 5 and I changed the bwa_index and bw_index_color.loc to the path
> /genedata/human_genome_GRCh37/hg19.fa

This is the problem - the path must point to the full name of the fasta file. 
In your case "human_g1kv_v37.fasta".

Using the name without the fasta as the base name in other fields as the unique 
"dbkey" is a good practice.

Hopefully this helps,

Jen
Galaxy team


> 
> 6 This is my $PATH
>> trr@portalmoritz:~> echo $PATH
>> /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19
> 
> Is there anything I am missing? I would be glad about some help.
> Best
> Moritz
> ___________________________________________________________
> 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:
>  http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

Jennifer Hillman-Jackson
Galaxy Support & Training
http://galaxyproject.org
___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to