Hi team,
I try many times, but I don’t know how to use online reference genome.
When I use bwa-mem.
If use own upload fasta.
bwa-mem will index fasta every time.
Could you told me how to fix it.
Very thank you,
Jacky
Hi team,
I try many times, but I don’t know how to use online reference genome.
When I use bwa-mem.
If use own upload fasta.
bwa-mem will index fasta every time.
Could you told me how to fix it.
Very thank you,
Jacky
I am not 100% sure so do some extra research yourself. But possibly you need this: https://toolshed.g2.bx.psu.edu/repository?repository_id=d4b644c94642cd8c?
You can install it from your own toolshed page.
Hi gbbio,
When I install data_manager_bwa_mem_index_builder.
Than results was same.
Source FASTA Sequence can’t find fasta file.
Do you know what problem is ?
And bwa-mem have same problem.
The bwa-mem can’t read fasta file (no matter I was upload fai, bwt, amb,ann, pac, sa file or not).
I am looking forward to your reply.
Jacky
Ah, I think I figured it out =) I got it working by installing data_manager_all_fasta_path
first:
https://toolshed.g2.bx.psu.edu/repository?repository_id=0a5e20872a520157
After installing you have a new data manager and trough this one you can add your fasta file. I only filled in the path field for the entry
field.
EDIT:
Can a developer now tell me how to remove the files again? =)
https://biostar.galaxyproject.org/p/13591/
Also see:
Thank you,
It’s work !!!
Could I ask other quation ?
In the local galaxy.
How to set threads when I use bwa-mem.
The command line only display “GALAXY_SLOTS”.
However I don’t know which config can set “GALAXY_SLOTS”
The machine have 32 vCPU but galaxy only can use one vCPU.
I am looking forward to your reply.
Jacky
The variable $GALAXY_SLOTS
contains a value coming from the galaxy/config/job_conf.xml
file. Here you can set the number of threads.
More info:
Dear gbbio,
Thank you your reply, but I can not found job_conf.xml in config folder.
It’s mean must change file name from job_conf.xml.sample_advanced to job_conf.xml ?
Then, rerun Galaxy ?
I can’t thank you enough.
Jacky.
Oh, yes you to need or can change on of the examples to job_conf. Think job_conf.xml.sample_basic
is easier.
Thanks gbbio,
Do you know how to set mutlithreads when we use bwa-mem.
Or job_conf.xml example.
Because tutorial doesn’t have.
Thanks,
Think you need to rephrase your question because I don’t think I understand what you mean. But:
Do you know how to set mutlithreads when we use bwa-mem.
This can be done by setting workers to 32 in the job_conf. If you set this to 32 the variable $GALAXY_SLOTS
gets this value.
Or maybe you can adjust the xml file yourself but I dont know if that is recommended. I dont see the harm in that but not sure. The xml file you find here I think galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa/somecode/bwa
your path does not have to be exactly the same.