I solved it so far :) Thanks for your help. On 26 July 2013 16:15, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Moritz,
Pls see below
On Jul 26, 2013, at 6:37 AM, Moritz Juchler < juchler@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
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