Question: MACS2 callpeak : MACS2_model.r not found
0
gravatar for plindenbaum
22 months ago by
plindenbaum90
France
plindenbaum90 wrote:

Hi all, I'm trying to use MACS2 on galaxy. It was installed on our local instance via the toolshed.

When "MACS2 callpeak" is invoked, there's a call to Rscript

## run R to create pdf from model script
#if $nomodel_type.nomodel_type_selector == 'create_model' and 'pdf' in str($outputs).split(','):
    &&
    Rscript MACS2_model.r > MACS2_model.r.log
#end if

But I get an error from Galaxy because there is no file MACS2_model.r anywhere (find / -type f -name "MACS2_model.r")

Any idea ?

thanks.

rscript macs2 • 700 views
ADD COMMENTlink modified 22 months ago by Bjoern Gruening4.8k • written 22 months ago by plindenbaum90

ok, as far as I can see xxx_model.r is created by MACS2... https://github.com/taoliu/MACS/blob/a3438e855d0e2824091168f03ee8586d59dbc5ae/DEBIAN/macs.man#L243

ADD REPLYlink written 22 months ago by plindenbaum90
2
gravatar for Bjoern Gruening
22 months ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Hi,

if I'm not mistaken this script is generated by MACS2 during runtime.

Ciao, Bjoern

ADD COMMENTlink written 22 months ago by Bjoern Gruening4.8k

Agree. For the problem, perhaps compare the R dependency you are using vs the repo requirements? You might consider reinstalling with managed dependencies to pull the version of R the tool is expecting. - Jen, Galaxy team

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson23k
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